Ideally, all the old code should be patched to test __HAVE_68881__ only, and GCC 2.95.3 should be patched to set that define. But it is a bit idealistic.
Why do you think so? It's matter of pure text replace, no thinking involved. I'm sure gcc 2.95.3 is similar to patch as 4.x, so no additional work for you. And I'm sure me or Keith or Mark or anyone can make a new RPM for us in matter of hours.
So I propose to patch GCC 4.x and *add* the nonstandard __M68881__ whenever the standard __HAVE_68881__ is defined.
It's up to you. You are our gcc god for Atari platform, so it always what you feel up to and how much work you want to invest into it... both solutions are nice.