> The recommending way to avoid this problem is to provide a patch which
> extends Isearch's handling of invisible text to text-properties.
> There's no reason to presume it would be hard to do.

See the attached.

> And the way I recommend to avoid this problem is to stay clear of
> indirect buffers (which I consider as an attractive nuisance).

It is not always possible. I am currently working on re-implementing
org-mode folding from using overlays to text-properties. However, it is
not possible to stay clear of indirect buffers in org-mode. Many
user packages and core code depend on indirect buffer functionality
(including different folding state). I will have to go ahead using my
"hacky" solution with char-property-alias-alist.

Best,
Ihor