I was wondering about the cheese on top. I wasn't sure if I should go ahead and buy vegan cheese at a health food store or not.
I have always made that dish with Daiya chedder shreds, and have not tried it with homemade vegan cheese, so I can't give an opinion comparing the two. I have used the homemade vegan cheese recipe for other dishes like baked potatoes or mac and cheese and it was awesome on those. I like Daiya though I only use it once every two months or so and don't rely on it as an everyday ingredient in my foods. It's sort of a special occasion type of deal. There are other commercial vegan cheeses you could try as well, such as Chao slices, or Follow Your Heart vegan cheese. I have not tried those.
If you can make a really good enchilada sauce, I'll bet you wouldn't even need the cheese. I've made many a vegan pizza without cheese. I will sometimes use hummus as a base, or a tahini sauce, or just a really good tomato paste/sauce and veggies. I was not a fan of dairy cheese back in the day and it made me so sick all the time I avoided it for many years, so naturally when I went vegan I didn't even try any commercial vegan cheeses for my first two years vegan. I would make a nutritional yeast homemade cheese sauce but truthfully it tastes nothing like dairy cheese. Or I would make homemade fermented almond or cashew based cheeses which are incredibly good but again are more like a dairy cream cheese than a straight cheese. I finally became more relaxed and started trying more processed vegan foods here and there a few years into being vegan because I was very underweight at the time and trying to gain, and also stop being so strict with so many rules about what to eat as a vegan. Long story. I still eat a largely whole plant food diet and very little processed, but I do keep vegan Just Mayo on hand, and occasionally splurge on some vegan "meat" or "cheese" products, maybe once a week or so. Some people love Daiya, some hate it, so it's one of those things you just have to play around with and see what you like and don't. I have still tried very few other vegan commercial cheeses to compare.
Another option would be vegan Tofutti Cream cheese or sour cream with that dish instead of vegan cheese. It seems to be much easier to find Tofutii products in larger chain regular grocery stores. Be warned though that the Tofutti cream cheese has hydrogenated oil in it, something I try to avoid, but they have a version of their sour cream that does not have that in it. Daiya also makes a vegan cream cheese that isn't too bad and is soy free for those who that is a concern with, but it is harder to find.