DASH build some amazing tools to improve fungibility, but I wouldn't say it's in the protocol...
I suppose that depends what you define as the 'scope' of the protocol. The masternode network are simply peers of the regular network which operate in a an alternate logic mode. Thats why they're often referred to as a second 'tier', or 'tier 2'. Their function is 'protocol level' enough to be subject to the condition of mining majority for successful adoption which I think is the significant criteria in that respect.
As far as I know, it's impossible to have a cryptocoin which doesn't have public balances for addresses
Doesn't Cryptonote do that ? In Cryptonote the balances are not public.