Take a half turn out of your lower limb bolt and see if it changes. Report back what changed.
I used to use bareshaft tuning as my sure-fire absolute final word on tuning, going all the way back to my recurve days in the '70's, but went to tuning for BH and FP groups being same POI, after having persistent difficulties in getting reliable results from bare-shafting with my full capture rests more than a decade ago.
IMO, all else is unneeded. Just make initial settings per manufacturer recommendations. Check brace height, axle-to-axle distance and any timing marks, set center shot and rest height as a starting place, adjust as needed in small increments to bring POI's together at forty yards, check at twenty to be sure adjustments still result in POI agreement, and you're good to go.
Arrow spine is only a factor (with modern compounds and past-centershot risers) if it's insufficient, and that will also be reflected in inconsistent POI.
Yoke tuning is something that needs to be considered only if you can't get the BH and FP POI's to the same spot. Same with fletch interference. Other steps in seeking perfect arrow flight are pretty much like waxing your truck before your western trip to get better mileage....might make you feel better, but there won't be any measurable difference. 8^)
nockup, Bowtechs will shoot excellent but set up nock level. It is ok to be a little higher through the berger holes if need be for rest clearance, but get it level. If you don't have a press, you have to try to address your issue with rest and loop. If bows cams are not in correct position to start, you likely will not be able to get the best flight, be it fletched, bareshafts, or broadheads.
If you have a press and draw board you need to check cam timing and cam starting position. There are reference marks on your cams, and the cables should be going thru those timing marks at brace. If the cables are not going through those marks as bow sits at brace, your cam starting position is off. Need to twist, or untwist each cable to get cam starting position inside those timing marks. Bowtechs are the easiest tuning bows but you will have the best results with a drawboard. After setting cam starting position you can now synch up the draw cycle of them. If you don't have draw board, have someone watch your cable stops very closely as you come to full draw. They should hit the same time. If one hits earlier put one (or one half) twist in that cable which will slow it down. this will allow you to have them synched up together. Continue until draw stops hit at same time.
This is true and I start as such in my drawboard. But....then I shoot a bareshaft. I do think that the board often hits a "little" different than the hand and can fool you...making you move the rest etc. In saying that-dont be afraid to twist the top or bottom cam to get rid of high/low tears or FBBH that are high or low etc. if all else fails. You think its synched but in your hand-as an example-the top might be just a bit off and thus cause low or high flight.
You can be off by 1/8 on cam synch and still feel like you have a good wall. Past that and you will "feel" it. However, it can affect arrow flight, at least to the degree of bareshafts an FBBH.
Cams are Synched in draw board. Rest right down the center and arrow level. Looks great...feels great...fieldpoints shoot laser .
However.....Bareshafts hit low with nock up (ie high tear). I dont want to move the rest UP because then I start with a nock HIGH position-not good :(
So I simply add one twist to the top cam (to slow it down ie make it hit AFTER the bottom by just a smidge). In board it looks like the top now is JUST a bit behind or hits after the bottom. But wall still feels good when I draw it and NOW.... the bareshafts hit level with the fletched arrows. If that happens-almost always the FBBH hit the same. as FP.
nockup, stick with it but keep that arrow level on that Bowtech and you'll get great results.
For me, while it's a good tuning method, I don't mess with bare shaft. I'll check things with paper and go right to broadhead tuning..... which is what I'm going to do as my final tuning anyway even if i bare shafted...... and personally I need every shaft I can scrape up to shoot stuff ... =D