Secret Police Center does not do exactly what the description says; I forget the specifics, but it's effectively useless. I believe it's 20% for one planet.
Harmony crystals are not bugged*, however you will have to re-adjust your tax rate to notice the approval numbers change, or force the game to update the numbers by opening Civ Manager and viewing your stats.
Incidentally, there does appear to be a bug, wherein trade goods built by another race do not give bonuses when you purchase them in trades-and this applies to selling them to the AI as well. However, if you build it yourself, that's not an issue, and if I remember correctly, only Gravity Accelerators were so affected.
TA changes things up a bit, yes, with the Yor in particular, with new dynamics for farms and morale, but you still don't want to go over ~20B per planet (with, literally, maxed out morale), or perhaps as much as ~22B per HW.
One of the biggest problems with the alternative trees, IMO, is that they barely have access to any trade goods-which contributes significantly to the morale shortfall you're experiencing.
However, as TA does add a number of race-specific mining and/or production modules, you ought to be able to fill in much of the gap if you manage to secure sufficient morale resources.