I haven't studied dosbox that much to know how it works.
In pmode with paging enabled, memory access is controlled by flags that
specify how a 4k page can be accessed. If an access is denied, a page fault
happens (telling that a page doesn't exist, is read-only etc.) and the pmode
extender/OS software part handles the information accordingly (like reading
the page from disk and changing the flags, then returning to user code).
The stuff that cares about the checks and that triggers the page faults is
in the InitPage handlers.
Simple example that may occur (that is not a memory sweep) is a stack that
is supposed to only occupy as little pages as needed, but may grow (almost)
infinitely. In that case the "next page for the stack" is marked as non-present
and if the stack hits this page, the extender/OS part allocates memory for
that page, thus the stack code works fine. The amount of memory reads
may be very large until such a page is hit.
I don't know if games use page faults like this, things to check would be
win3x (surely uses it) and some heavy games (descent, borland extender games).
So the rewrites that remove handler checks (the
3) most accesses are direct (positive treshold is reached) -> the code is rewritten to access the memory directly - here is the speed increase
part) will introduce problems for certain games, but i don't have any clue
if a large number of games would be affected (i'd not expect that).