The whole tragedy of jmart is that they would've never worked out, no matter what situation they ended up in.
In their current situation, Martin can't bring himself to love Jon fully and honestly because he finds the "monstrous" part of Jon repulsive.
If Jon hadn't become an Avatar, then the others wouldn't have resented him and so he wouldn't have turned to Martin in such a desperate attempt to maintain a connection with humanity.
If they hadn't been working at the Magnus Institute, then they probably wouldn't have looked in eachother's direction twice, and they definitely wouldn't have formed any meaningful bonds.
MAG 199 - Seeing It Through
The canon timeline is possibly the only scenario in which they ended up together, and they both know it. They are holding on by sheer willpower. Their relationship is a carefully balanced structure just one precise jab away from crashing down.
And I think there's beauty to be found in that. How they both claw desperately at one another to remain stable.