A couple tips from a dude who uses that exact toolchain for everything:
Fusion 360 uses the G28 position of your machine for each operation. M6 tool changes go there, as does the beginning of each program. I reset my G28 fairly often, based on what fixture I’m using. For me, I’ve found that with a L-type fixture that orients my stock repeatably in an exact position, having my G28 set to the corner of the fixture, and 2mm below the homing position on the Z seems to be about ideal. To set G28, just home your machine, jog your spindle to wherever you want it, and send G28.1 From that point on, any time G28 is called, the spindle will go straight back to that position. Be aware, that if that straight line goes through clamping hardware, etc, the machine will very happily slam right into it. Watch your clamps!
You are correct in that ChiliPeppr offers the touchplate feature, which does just that. If you have a touch plate equipped, you can zero your Z automatically. If you don’t have one equipped, you should do so immediately. It’s a massive improvement!
Build a fixture! I’ve found toggle clamps and a pair of perpendicular stops mounted on top of a piece of 3/8" MDF to be of incredible help. Saves me an absolute ton of time, and saves the wasteboard from being screw-perforated all the time.
Congrats on a good run!