Pete I’m unclear as to why using butyl tape cause “stripping the fiberglass during installation”.
I'm not Pete, but I can take a guess. I have found that if you have a "pointy screw" going into a solid substrate, and then you try to compress something like butyl (especially in cold weather), you can strip not the screw, but the substrate with the force needed.
Unless there is some overriding reason it's not possible, I will always choose to through-bolt, or least drill and tap thickened epoxy (if no access to backside).
Obviously stanchions should be through bolted with the force they are subjected to, and in that case butyl would be fine, in my book (Bed-It brand is the best I've found).
I also would say there is a point to re-bedding even if not leaking, because then you can epoxy pot the opening and try to avoid future core mush issues (if cored). It's much nicer to do it in advance than after things have rotted.
OP: That certainly looks gnarly. Will be so much nicer when you get it squared away.
We all have our own preferences. I like to clear out the balsa and fill with thickened epoxy. Then I install the backing plate, my preference is pre-made fiberglass board (plain or G10, I buy at Mcmaster Carr). I adhere the backing plate to the underside of the deck with an epoxy mush (keeping it parallel with deck), then drill right through both from on top and through bolt. Of course you don't always have the access for this, and too, other things will work (stainless, etc.). I avoid Starboard for backing plates as it creeps under load.