Curate, connect, and discover
If there is one thing that I wish the entirety of gravity falls' fandom all knew is that Ford was not trying to separate Dipper and Mabel before weirdmageddon. Especially not for a dumb reason like "He's self projecting onto them too hard"
Because
1) Mabel resembling Stan??? Not only is every cannon interaction between them positive, but even if Mabel reminds him of Stan, she would remind him of the version of Stan that didn't ruin his future, just the version that liked fun and cared. The version he very dearly misses.
2) Where in the show does it indicate he doesn't apprentice her for such a reason?? Is it just headcannon?
Because one thing the show makes abundantly clear is that Ford has major trust issues due to his trauma. I wouldn't blame him, as his main and really only support system after Fiddleford's portal incident ended up wanting to tear his world apart due to their strong denial. That is a tangent I won't be getting into. BUT the show could not make it clearer he has difficulty trusting.
The reason he would want to apprentice Dipper is because he showed him a deep paranoia that he also shared, and since Ford learned that paranoia is good as it keeps you alive from Bill, this is a great thing. That's why he praises Dipper for almost memory wiping him, as he saw Dipper capable of defending himself against Bill Cypher's manipulation. Also, in the episode that Ford proposes that Dipper should be his apprentice, Dipper also proved he could handle highly dangerous situations, meaning he could handle some of the things Ford learned to handle. Dipper showed Ford he could be trusted as he wouldn't get manipulated by Bill or be killed by the environment.
Mabel, while he really likes that kid, is very emotional and empathetic. One thought I could very easily see Ford thinking is "Mabel could very easily be manipulated by Bill Cypher" She might have the physical might (refer to the mabelcorn episode) but it alone cannot protect her from Bill, as he is a MANIPULATOR. What if he reveals information to her that could be fuel to Bill's manipulation? Being Ford's apprentice would mean that you are likely to deal with Bill too because he just won't stop tormenting him, and saw that Dipper was the only one that could truly handle the dangers of Bill Cypher. If Bill somehow possesses him, he knows Dipper would do the right thing, and he knows Mabel would hesitate.
Separating them was a consequence he didn't forsee as his reasoning for offering apprenticeship to Dipper had nothing to do with the twins' relationship, and it would make Mabel trusting BlendinBill because Ford told nothing to Mabel that much more thematically better. The show is about trust, and due to Ford's lack of trust in his family, it ended up endangering them.
Tell me, what is more satisfying? Ford maliciously trying to create a gap between the twins for no good reason or a traumatised Ford with trust issues learning to trust? THE ENTIRETY OF THE WEIRDMAGEDDON TRILOGY IS ABOUT TRUST, WHY WOULD IT BE KICK-STARTED BY ANYTHING THAT ISN'T TRUST RELATED?????