There is hope for "Save into individual files" on flatpak package - please see this !
Hi. This issue on behalf of discussion that was made within #20 (closed)
It seem that it is quit possible to make the new feature of [Save to individual files], that you already disabled on flatpak by commit 98a2f76f, it is quit possible to make it active on flatpack package also !
I tested other flatpak application called "nomacs" which has similar functionality called "export multi-page TIFF":
Tools | Export multipage TIFF
This functionality allow user to extract multipage TIFF image into individual TIFF files (same as of your "Save to individual files" sub-option of "Extract pages" functionality. I test nomacs "Export multipage TIFF" option on a 500 pages multipage TIFF image & it worked without any error & it extract 500 pages of single original multipage TIFF into corresponding individual 500 TIFF files.
Kindly, review this issue.
Many thanks for your very hard efforts & patient.