The same is true for two Rikers. That’s the entire point of the episode; that despite them diverging at the point of the cloning into two different people, they are still the same person and need to live with that.

I don't think that as the point of the episode. As their lives diverged their interests and desires did so as well. They were similar, yes, but still different people. Will was promoted after successfully evacuating the people of Nervala IV and he became focused on his career. Thomas was stuck on Nervala IV thinking of the woman he left behind, and when he's rescued he wants to rekindle that relationship whereas Will let it fizzle.

To say nothing of Thomas eventually choosing to join the Maquis. That is not something we'd ever see from Will.

Will: Good luck, Will.
Thomas: I actually thought I might go with the name Thomas.
Troi: Your middle name.
Will: I guess we really are different. I never really cared for that name.
Thomas: Well, I sort of like it. I guess I'd better get going.