Unbondable rabbits?

Has anyone not been able to bond 2 rabbits even after doing the "proper" bonding process?

Yeah. No matter what I tried, my two female buns just wouldn't get a long. I worked at it for months, tried all sorts of different things. Finally gave up, split up my other pair and bonded one with each of the girls, which worked out fine.

Some rabbits just don't like each other and never will.

My two hate each other at the moment (really my female hates the male) and they just have to live as single bunnies for now. It can take a long time to bond (I refuse to just give up since I can't exactly get other rabbits for them- I'm at my pet limit for my apartment) and returning either of them is not an option (they were both on euthanasia lists for behavior issues).

Humans are the same way- there are just some people you don't like, and probably never will.

Yes, it happens sometimes. It's more frequent with same sex couples, but it can happen with male / female too. To begin with, some bunnies hate rabbits. I've known a doe who couldn't stand to share her space (I remember the woman who had her saying that she binkied like crazy on the day her two other rabbits were at the vet for their spay / neuter and kicked up a storm when they came back home) and tried to gut every rabbit she met.
There are also rabbits who just can't stand each other. Aki hated Tybalt when she met him - he is dirty and lazy and can't be arsed to follow the correct rabbit etiquette whereas she's a complete neat-freak and very dominant. They got over it, eventually, but I really thought it wouldn't work.
Sometimes, you need to persevere. I'm pretty sure there is an article on the house rabbit society website about a couple that took several YEARS to bond. It worked in the end, but it was very difficult (I admit, I would have given up much sooner).

What is the concern of trying to bond a neutered male with a not yet spayed female? Or a just spayed female? Is it just because they have a higher likelihood of Not bonding and fighting because of the hormones?

I am going to be getting my bunny spayed soon, hopefully within a month. But I feel so bad for her because she is bored and very social at times and getting into everything I'm doing. Like really needy. I know she really needs a friend for company.

I found a male rabbit I was thinking of adopting. It's hard for me because I can only have rabbits that have wool because I'm allergic to their fur. So finding a wool rabbit that needs adopting is not easy. So when one popped up, I want to jump on it.

Males can be fertile for many months after being neutered, so if you don't want babies, be careful! That's the main issue. Further, if you bond them and then change their hormones by removing the hormones, you can damage the bonding process. (Side note- I love that you are getting her spayed!! That's great!) If it were me, I'd get her spayed before getting a male if it's possible (sometimes, the perfect one just pops up and it's not )