I was thinking about doing this myself (although I've decided that for now the benefits are not worth the work).
I feel that the best approach would be cutting a holder for extra clearance around a specific format, and using
appropriately sized mylar (or whatever material it is) to sandwich the film, taping all around and using the
magnetic flap for support. As I see it, stumbling block one making a reasonable punch and die for a 4.25" x 5.25" hole,
or in your case 26.5mm x 38.5 mm. Stumbling block two would be making up a mounting bench, because the
idea of naptha/equivalent getting all over the scanner doesn't have a lot of appeal and there isn't all that much
room to work with the holder on the scanner (for the taping, squeegee-ing and such).
Instead I've gone with higher diligence on predusting the film manually, and finishing up with copious electronics duster.
However, as you say for archival work and thoroughly (though lightly) scratched materials that wouldn't be enough.
In my case I'm luckily working mostly with recent work (90% my own/gf's), and from people who bring it to me straight from a lab or
a well looked after archive.