Mech, of A4000T.com fame says that 64GB is about where the Amiga functions at its top limit of CF cards. The Amiga firmware has a boot partition limit to 4 GB and many programs (ReOrg, DiskSalv, etc.) use this limit as well. Once booted the HDD limit I had was 2TB, that is the largest HDD I had to test (one of five 2TB HDDs in my PC -- DVR'd movies). This was seen in OS 4.1 and 3.9.
On the Amiga, I believe if one needs a larger boot partition, one may wish to reconsider WTF it is being used for. Only my biased opinion though.