You seem to have the idea, but you're confusing step 1 and 2 as two competing alternatives. The VERY basic concept of bareshaft tuning, even though it's still a point of debate amongst some, is this BASIC process:
Phase 1
1. Set plunger TENSION to ROCK HARD firm (replace spring with a matchstick so there's ZERO give).
2. Set plunger POSITION to DEAD-CENTER, so the arrow looks right in line with the string down centershot.
3. Shoot fletched and bare shafts and adjust limb weights (with limb bolts) and/or arrow components (point weight, etc.) to get the bare shafts to impact with fletched.
Phase 2
1. Set plunger tension to a medium setting (middle weight spring and about middle of the in-out spring tension adjustment).
2. Set plunger position to place arrow centershot just outside (left for RH archer) of the string (base of the point should be just appearing to touch the string down centershot).
3. Shoot bare and fletched shafts and adjust plunger tension to get the bare shafts to impact with the fletched.
Recognize there is a bit more to it than that, and the list of things you can adjust is very long (string weight, strands, material, nock point (brass or tied-on), fletching weight, size, wraps, point weights, etc.), but this is a basic premise of bareshaft tuning. As I understand it. Took a while to get the hang of it, but my new arrows are finally tuned BEAUTIFULLY, and it was well worth the time, trouble and frustration to learn it.
Best of luck,
Ted (me, not you...)