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A:1 - 52/4200 is an adhesive first, sealant second. You just need to overpower it. Drive the bolts out.

A2: Do not use an adhesive anywhere on the boat, unless you are fabricating something. Use Boat Life's Life Caulk for everything sealant related.

Seal the transom holes walls as a precaution and under the washers.

A3: All that needs sealed are the holes in the transom. The engine bracket does not need to be sealed.

When my new engine was installed by a factory trained tech in 2020 he hung the engine, coated the hole walls, inserted the bolts with the engine an inch off the transom, placed a bead of sealant under the washer on the inside of the transom and on the outside.
When he tightened the nuts the sealant oozed out from the inside washer. It oozed out near the top bolt and the lower hole in the slot.

Is this clear?