Actually we kept 8.3 till 2015 because of plain dos, but it was untenable to keep such limits forever on all targets.
What version was that? If OP specifically wants to compile natively it would be worth his while investigating what's changed since both in the core libraries and extra packages.
3.0.0, together with win9x support; but those don't support m68k/Atari. But even those older versions had little kinks due to limited plain dos testing.
I think the first step would be to find out what Atari community has to offer for such problems, that are not unique to Free Pascal(e.g. dos worked on a doslfn driver for a while).
Otherwise you are limited to using the filesystems that can or cross compile. (and since recompiling FPC takes 8 minutes on a RPI4, I shudder how long it does on Amiga. Even a small twenty years ago, with FPC 1.0.x on Mac 840AV (the heaviest retail m68k machine from Apple with a factory overclocked 68040/40 + 128MB of RAM, more than oldies typically have) it iirc took 35 minutes.
added later: or maybe I misunderstand and there is a way to do lfn support, and must it be added to the RTL