Yes. So ideally, you would use just three lengths of thread to do the sewing. I think, if my memory is right, I was short on my bow thread too. That means you have to pull a knot through your fabric causing bigger holes in that area. The long thread sounds cumbersome but it isn't really that unmanageable.
I have no opinion on the tape other than I like the sewing method just fine.
Todd, I don't claim this is the best way but this is how I did my deck bungy fit.
Made loops from webbing - cut a length, folded and then melted a hole through. Used an old soldering gun for both cutting and making the hole. Best to use polypropylene rather than nylon - uncoated nylon usually has less resistance to UV light.
Screwed loops to side of gunwales - not the top. Two reasons for this: 1) side is wider than top so less likely to split the timber due to being too close to the edge, 2) I believe there is a slight mechanical advantage with the loop going around the edge of the gunwale.
Either use a wide headed stainless screw or a stainless screw and washer.
Bungy installed: