Finished the job last night. Never figured out what the velcro was for. I never dismounted the plastic guard on top of the frame that the outer cover ridge slides into (the plastic guard is strapped in with a metal clip I didn't wanted to pry out); perhaps the velcro is for re-mounting this part...
Either way, the job was fairly easy (but annoying!). I'd like to offer a few comments since all other comments online seem to be in favor of aftermarket outer covers with glass windows and defrosters:
The original Porsche outer cover fits perfectly and all holes are pre-punched and all edges are cut and trimmed to perfection. The cover comes with metal plates, springs and wires, rear rubber and plastic linings, foam side linings as well as parts 986561559/560 for mounting the bottom of the top. Those are plastic parts that I imagine are beat up on many Boxsters although they were in good condition on mine and wouldn't have needed replacement. Anyway, it is significantly easier to mount the new outer cover when mounting on these parts BEFORE they are attached to the car frame. With the original cover, there is no need to reuse any wires, springs or metal plate parts. The new metal plates come with adhesive and you can reliably glue the canvas on by aligning the pre-punched holes before even putting the top on the car. The cover simply fits perfectly. There is no trimming of corners or along metal plates. There is no need for spray adhesive (I did use one strip of double-sided tape and two beads of black rubber adhesive). There is no need to stretch the canvas to get rid of bulges etc. It simply just fits! It's a Porsche product! However, this was never intended as a DIY part; it comes with NO instructions whatsoever. It is, though, much easier to mount than aftermarket kits (think Porsche wants this replacement to take as few shop hours as possible for a dealership mechanic!).
Now for the plastic window: If you choose an aftermarket cover with glass window, it will significantly be in the way when in service position and your access to the engine from the top is going to be significantly restricted. My car has ~160,000 miles on it and I spend a lot of time accessing the engine! I prefer to have full access. Also, I have not even once thought to myself: "I really wish I had a defroster in my summer roadster". I simply don't need a defroster. The plastic window is much larger than the glass version and your field of view is thus much larger and there's more light inside the car. I like my car OEM as Porsche designed it. My 2000 Boxster rolled out of the factory with a plastic window and I like to keep it as original as possible. When I look on youtube, it looks like even quite new canvases get sharp wear-lines radiating from the corners of the glass window. I imagine the canvas takes a beating in EXACTLY the same spot every time the top is lowered because the glass window is rigid. The longevity of the plastic window is obviously lower compared to glass; my car is 23 years old and I just replaced it (although it should have been done 3 years ago). Even so, my plastic window had a lifespan of 18+ years. The new one will probably last longer as the car is always parked in garages and only gets sun exposure when I am out driving. To me, it's simply part of maintenance that the outer cover must be replaced every 15-20 years. I doubt the canvas on a glass window top is particularly attractive at this age anyway.
Not trying to tell other people what to do or that they are wrong in their choices, simply offering a different perspective on choosing the top outer cover replacement that fits your needs!