I see no problem at all, as long as the installation is done properly, and the hatch of good quality that seals properly. If I was to use a salvaged one, I would surely ensure its integrity. You can buy new custom sized ones at a reasonable cost, giving you the most effective sized opening you can get. You have done it before, so it should be no problem. Does it look as good as without one, probably not, but in most cases the convenience it affords is very much worth it.
I replaced the stock on on my Escape
19 with a much larger one. It was easy to do, and works great.
Old and new hatch covers.
All laid out ready to cut. I used a jigsaw for most of it, and a bit with a dremel. I did have to do a new cutout to move the electrical
Holes all cut. After sealing the flange to the body, I fastened with rivets.
Newly installed hatch. Easy peasy.