I'm not going to comment on whether Mindanao is dangerous or not, I am not an expert on that and couldn't say.

Just a couple of things, first if the NPA are really what they claim to be, they shouldn't really care less about foreigners, unless they were involved in economic activity threatening to locals. Of course, things get twisted and perhaps they are.

The bigger thing - a bomb goes off in Istanbul, some tourists get stabbed in Marmaris, and Turkey becomes unsafe for tourists. Some separatists in a region of Turkey have a shoot-out - despite that region being further away than the UK is to Italy, then the beach resorts overlooking Greece become unsafe to tourists.
Demonstrations in Bangkok and the government advises against going to Thailand............all of Thailand.
Someone sets off a bomb in Mallorca - does the home office advise against all visits to Spain? Do they advise on avoiding Magaluf - do they hells like.

Selective much?