Meanwhile, you can still use Hook to copy links from any supported app, and paste them in OmniFocus comments. This is actually what I prefer to do.
And as a stopgap, you can use OF’s own Copy as Link function, and paste in source if possible (e.g., in in markdown docs).
But again, it’s a priority of ours to sort this out. More generally: to ensure that all versions of any supported app function regardless of whether they are from Mac App Store, the vendor’s site, and Set App. (It’s generally working well, but we want to keep exceptions to an absolute minimum, like zero).