Thanks for the hint! I might work on this issue on this weekend. I should check about how much symbolic link is too much, since it might be abused and/or cause malfunction.
I created an ad-hoc patch for this issue, check this brach. Part of it is a duplicate code of Thunar c7fa6320, which I will deal with later.
@flashwalker I verified it by installing flatpak and floorp(system). Now it complains about permissions but it seems to work fine. Does it work for you too?