No, I absolutely agree with you that Jon acknowledges the threat that Tom would be if matched up against him, but Jon isn't motivated enough to fight. Usually a challenge excited Jon, but now a days he feels that he has nothing left to prove anymore, so fighting a dangerous guy like Tom while not being motivated will potentially fuck up Jon's legacy.
Look at BJ Penn. When motivated, one of the baddest ever. Same with Rampage Jackson. Jon took the easy fight against Miocic but Tom is a threat, & while not being motivated enough since he feels he has nothing to prove he isn't going to take a fight that can hurt his legacy especially right at the tail end of it.