You still need to keep every partition under 1Gb for 2.x Workbench version's FFS. For 3.0/3.1 you can use partitions up to 2Gb (Amiga DOS problem).
Anyway, more than 200Mb for the boot partition is nonsense. If for some reason you manage to de-validate it it will take ages to fix itself.
Since the A3000 have a 030 CPU (or better), install and use SFS in the others.