Does Indigon work with Blood Magic?

Which part of it?

"for each 200 total mana you have spent recently" specifically tracks mana spent. If you spend life instead, it won't trigger.

"increased mana cost of skills" is transferred to life cost of skills too, since with BM you pay life to cover the mana cost.

Stuff that affects mana flasks still only works for mana flasks, even with BM. (With the BM keystone you can't have non-instant mana recovery though.)