I have some soulgem mod that makes them not recognized. Doesn't really matter, real quests can be bypassed with console commands (Dwemer boots of flying aren't noticed either but, meh). But I'd like to go further in IO -- it is such a wonderful mod. Does anyone know the console command for bypassing the ancestor ghost quest?

Are you sure you're soultrapping a vanilla Morrowind Ancestor Ghost? Because I got stuck on a soulgem quest in another mod when the questgiver wouldn't take the rat souls I trapped. As I was putting them into a container, I noticed I had rat souls worth different values.
Turned out I'd been trapping rats added by a creature mod. Consoled in some rat-filled soulgem (using the creature id listed on the UESP) and the questgiver accepted them.
Try:
player->addsoulgem, ancestor_ghost, misc_soulgem_common 1

It's been awhile since I did that quest, so I don't know what gem size you need; just replace the word "common" if it isn't the correct size.