I think it is more real than you realize.
For Heyward, I just don't see it. And he's not even the problem. He's one of the best situational hitters the cubs have which as I mentioned is their problem. In high leverage situations he's hitting .256/.348/.385(101 wRC+) which is 4th on the team if you assume Murphy is gone and better than the 98 Bryant has. If you have an issue with Heyward it's because you view him as a RF. You really shouldn't. IMO you should view him as the starting CF who moves to RF occasionally. Viewed through that lens you have a gold glove caliber OF who's an average hitter in CF. That's a pretty valuable player.
Those moves just don't make any sense to me. Hamilton is a career .245/.298/.333 hitter. He doesn't make the line up better. Harper might be better than a Almora/Schwarber platoon but it isn't as big a gap as you think it is. If you strictly view those two as a one player platoon they hit 85-352 with 11 doubles, 3 triples and 25 HRs to go along with 64 walks and 112 k's vs RHP and 39-132 with 9 doubles a triple and a home run to go along with 9 walks and 16 k's vs LHP. Combine the two and you get 124-484(.256) with 20 doubles, 4 triples and 26 HRs which is a .475 SLG and a .352 OBP. Harper hit .249/.393/.496 this year compared to that combined slash of .256/.352/.475 of Almora/Schwarber. Sure you probably take Harper all things being equal but they wont be. Schwarber/Almora are likely making under $2 mil and Harper is going to get like $25-30 mil.
Additionally, Machado makes far more sense if you assume Russell is getting suspended than harper would. Sure you can play Baez at SS but he's better at 2B and either way you have to have someone else on the roster who can back him up if he's hurt. Machado is perfect for that and his low K rate fits far better into the line up than would Harper's high walk rate higher K rate great power type bat. I mean if you have issues with Schwarber you're going to have the same issue with Harper. They are very similar hitters. IMO you want more hitters like Rizzo/Zobrist who put the ball into play with guys on base rather than walk or homer guys. Plus unlike Harper, Machado will not cost a draft pick to sign.
I think you're over thinking all of this and trying to blow it all up rather than addressing specific issues. Almora/Schwarber is a perfect example of a small change that costs you nothing to make but can have a big impact. Playing Heyward more in CF where his bat profile fits better is another that costs you nothing. Allowing Zobrist to play more is yet another whether that's in RF or at 2B with Baez at 3B and Bryant in RF. I just think the big move you make is replacing Russell as the starting SS with Machado. You're likely going to need a different MI anyways if he's suspended and if you're willing to spend the money on Harper then you're willing to spend it on Machado instead.