1) Their bonding in Friendenemies: This is part of the "ram all the pieces together to finish the puzzle." The whole guise of Tom wanting to hang out with Marco was to earn a badge. One that meant he had to hang out with the person he hated the most. So all of those "bromamce" moments come with an asterisk. They’re artificially made by Tom to keep Marco engaged long enough so he wins.
2) Raising Mackie Hand: Tom knew Marco was going to tell Star about what he was up to. Tom diffused the situation so Marco's report to Star didn’t cast him in such a negative light.
3) You're My Best Friend: Tom says this to Marco in Conquer, but Marco does not return the sentiment. Instead he confesses that he kissed Star. Tomco shippers will tie this into a late Season 4 episode where Tom says he needs to date his best friend. A) It was not a callback to Conquer and B) In the VERY NEXT EPISODE Tom tells Marco he should date Marco's best friend, Star. That was the point of Tom’s comment.
4) They have great chemistry: Really? Gaslighting, deceit, kidnapping, being held hostage, having a curse put on you to embarass yourself? That's not great chemistry. And, yes, they did try and bond over Dragoncycles. But that only led to Tom figuring out more about himself, not about stronger ties to Marco romantically.
5) The Duet: When all else failed, Marco ran a talent show waiting for Star to return in Coronation. This was probably the only time that Tom and Marco appeared as genuine in the entire show. The segment lasts less than 30 seconds. Now, add up all the time Star and Marco showed chemistry.
6) The pieces don't fit: In the end, Tom and Marco are on friendly terms. But this is a show for young people. Mistakes are learned from and characters move on to what's right for them. Tom and Star and Tom and Marco don't work. A lot of the out of context scenes spliced together in fan videos don't show the big picture behind the dynamic that is Tom and Marco. Starco had an arc. Tomco didn’t. It was deceit and lying at first and then Tom working on himself for Star before realizing who really had her heart. Disney didn’t stop it. It was never the plan in the first place.