Using one continuous abrasion patch layer over the whole hull and the hull/deck joint will work perfectly fine. I do this myself sometimes. I am willing to accept a slight weight increase in exchange for a stronger kayak, faster and generally much better finish. You will need to mask the sheerline off and make sure the glas adheres the required distance past the joint. Sometimes this requires a relief cut in the glass. This technique cuts DAYS out of the construction so it is definitely worth it.

If the epoxy job on the first glass layer is too lumpy due to the premature epoxy hardening, you may want to knock it down with a sander because the lumps and the new glass layer will trap a bit more epoxy (more weight).
The finished surface will be also more 'textured' which will require some sanding and cutting into the last layer of fiberglass (unless you add significant filler layers to bury the imperfections - more weight still).

I have found that over the long term, sanded through fiberglass weave may also become more visible (the sanded weave turns opaque white).

Also, it is very likely that you will need to fill the hull/deck joint since the shells (hull & deck) rarely seat without a few narrow gaps.

I hope this helps

Vaclav