As long as the modded player-crises don't alter is_player_crisis then the vanilla Nominate Custodian Resolution will work.

The modded version for a Crisis Nominating themself was originally designed to check vanilla player crisis APs, but I'm adding "has_country_flag = DCC_valid_crisis_for_custodian_resolution" to allow it to target any empire with that flag. All a modder would have to do is flag an empire with that flag, telling Nominate Crisis Custodian resolution to work.

As for any modded crisis opinion penalties, the "Defender of the Galaxy decays Crisis Opinion" is receiving a new check "has_country_flag = DCC_valid_crisis_for_dotg_decay" so any empire with this flag will count as a crisis. Unfortunately this decay cannot modify opinions added in through other mods, but I can modify triggered_opinion_crisis_empire to occur for empires who have specific flags. This would mean another mod could set flags to determine what crisis level a crisis has reached in order to trigger opinion penalties added by this mod.

If a country has these flags they will receive the corresponding Crisis Opinion Penalties:
DCC_valid_crisis_for_opinion_penalty_level_1: No Opinion, prevents hating other crisis empires for them being crisis.
DCC_valid_crisis_for_opinion_penalty_level_2: BASE -60
DCC_valid_crisis_for_opinion_penalty_level_3: -140
DCC_valid_crisis_for_opinion_penalty_level_4: -240
DCC_valid_crisis_for_opinion_penalty_level_5: -400
These values will be modified by the scripted decay this mod adds.

Currently how this mod works is it adds a scripted effect called begin_triggered_crisis_opinion_decay which will start the "forgiveness" process, reducing the opinion penalties. It is fired every month by country_event DCC.10 and causes empires who know a crisis empire is a crisis of at least level 2 (DCC_valid_crisis_for_opinion_penalty_level_2 and witness country has level 2 intel on them) or level 5 (DCC_valid_crisis_for_opinion_penalty_level_5, no intel requirement).