MD5 is not used bu OpenPGP. It is allowed for backward compatibility but even
that has been dropped for GnuPG 2.1.
The use of SHA-1 fingerprints is hardwired into OpenPGP and to change this a
complete new key format needs to be specified. In any case the fingerprints
are not a problem right now.
Using Base64 fingerprints are actually a bad idea because they are to hard to
compare for a human.