I have refused to reply to any message targeting my lesbianism in regards to Neuvia due to the constant harassment I have been facing since I started to draw them together, but since your message is worded very politely and you seem to not look for any violent confrontation, I will make an exception for you and you alone.

First of all, yes, I am a trans lesbian. I never hid this part of my identity on my Twitter profile and while it is not something that is primordial to acknowledge to enjoy my art, I think it is still something important to bring up for others to understand that I might be more vulnerable regarding a few specific subjects.
You probably never interacted with me prior to my Genshin (or even Neuvia) fanarts which is completely alright, but just so you know, I have never been opposed to M/F ships and have been really into a few of them since years, alongside some M/M and F/F ones. The thing is, art-wise, I am usually driven by whatever my friend Phel enjoys, and despite him being a gay man, he can also be fond of M/F pairs just like anyone enjoying shipping. Whenever he gets into something, it makes me happy to make some art of said thing for him, and it does not have to go deeper than that.

Regarding Neuvia, I was aware of the Wriolette and the Clorivia ships even prior the release of Fontaine. However, I did not really care much about it because at the time, Genshin-wise, I was mostly into Dottolone and the only Fontainian I was excited about was Arlecchino. However, the moment I played the 4.0 AQ by myself, I became obsessed with Navia who quickly entered the Top 3 of my favorite female characters of Genshin (alongside Rosaria and Nilou). And funnily enough, I was not that charmed by Neuvillette at first; I guess I expected him to be like Zhongli so I subconsciently prepared myself to dislike him, but he was... Alright.
I then discussed of the AQ with Phel who sent me a few fanarts of Navia, some of them being with Neuvillette. It made sense to him and me and it was "there", but because Phel tends to grow very passionate about very few things and seemed to really like them together, I started to draw them for him. I also remember him sending me a very cute fanfic of Navia and Neuvillette visiting Mondstadt together which more or less cemented the idea that they would be cute together to me. Then the 4.1 happened with Neuvillette's SQ with a cameo from Navia, and the rest is history.
(unpopular opinion incoming but the 4.2 AQ disappointed me greatly and more or less destroyed a lot of interest I had for various Fontainian characters, but I did appreciate the moment when Neuvillette saved Navia with the help of Melus and Silver, although I do think it was not that well done in some points. But this is another discussion I do not feel like sharing publicly)

Still, you are asking me: is Neuvia born out of a lesbophobia and/or homophobia? Maybe, I genuinely have no idea for I have never been into online communities to be kept aware of this kind of thing (and ngl, I actually actively try to not get involved in them because I find it very miserable in the long run, here talking from experience after spending many months in a specific community back in my Overwatch days), but I can assure you my affection for them has never been grounded in any hate toward anyone.
I personally see and depict Neuvillette as a he/him butch lesbian, not to try to "pinkwash" Neuvia but simply because I am butch myself and it makes me happy to do so. And I obviously never saw Navia as something other than a sapphic (a femme lesbian in my case but I also vibe with people seeing her as bi/pan!). However, I fully understand people not liking the ship and/or my headcanon and it is all fine and dandy, for I refuse to push my very own personal viewing of something bringing me joy onto anyone.
The thing is: I do not represent all Neuvia shippers, and I barely interact with them beside RTing a few fanarts of them every once in a while. Are they bigoted? I will be honest: I had the displeasure to deal with a big chunk of them being openly LGBTphobic, "even" toward me (in the way of "hate the sin, love the sinner"). But I do think this has more to do with the fact that I am a lesbian before being a Neuvia shipper, and my lesbianism does impact my vision and depiction of them in some ways.
I blocked them, just how I block anyone with views I disagree on, but I fail to see how I am responsible for them being against the existence of a group of people I am a part of. In my eyes, shipping is not activism and should not be treated as such, but I do refuse to believe some M/F ships are born out of spite of a M/M and/or a F/F ship. For me personally (as well as Phel, remember, we are making art together), it is not the case, but it would not surprise me it would be the case for some others.
(and while this is not the main subject there and I do not want to point fingers at others to divert your attention on the important matter of lesbian erasure, I feel the need to bring up that shipping a M/M or a F/F ship does not exempt one of being a bigot, for you can also be bi/panphobic, transphobic, racist, misogynistic, ableist... And even butchphobic! And let me tell you it is never a great feeling to think your existence as a butch will be considered as a threat by other lesbians and sapphics)

Finally, I do not like to dwell too much into personal matter on my public Twitter but I have offered nothing but support toward any person who had to stumble across the corrective rape fanfic you are talking about and it pains me to remember its existence for it is something I have been a victim of. It is even more painful when I have received multiple messages, thse past few weeks, wishing me to get correctively raped again for not shipping Clorivia and/or Neuvifuri because I guess I am such a fake lesbian for liking Neuvia, I should just become straight at this point.
It is an extremely sensitive subject to me and I probably met many Neuvia shippers with hostility when said fanfic came to light because I was so fed up with them bringing up how our ship will most likely become subject to hate in lieu of being shocked that something like that would ever be published, untagged and only made with the intend to shock and trigger lesbians and sapphics. I think it would be more rewarding for many people to target our common oppressors rather than lashing at me for apparently betraying my kin, but it is just so hard for me to form a coherent thought regarding this specific issue without growing angry and hurt all over again.