I've done it both ways and you covered the pros and cons. Since I'm getting older not younger I would now lean toward the trailer. Plus, when I put them on the roof I had the lower pop-up too. My hard side roof has too many obstructions plus I really don't want to stand up there pulling up the kayak and lashing it down. Actually thinking of getting a Pakboat folding kayak and not have to get on the roof or tow a trailer.
I tried it using Whazoo's method and it didn't work for me, although his canoe is much lighter than my kayak. Plus, the lower pop-up roof makes swinging the boat up much easier.
I carried one large tandem Hobie Oasis on the roof and didn't remove it to raise the roof.
YMMV