functions identically to a wizard’s bonded object except it can be used to cast cleric and domain spells (instead of wizard spells) and the ecclesitheurge can grant his bonded holy symbol only magic abilities appropriate for a holy symbol or a neck slot item.
I can't find the text saying that you can't have both a bonded object and a familiar, but I could have sworn there was text to that effect somewhere. So, the answer may rely on how that text is worded.
As long as you're not using Sorcerer Arcane bloodline (which specifically says no) to acquire the familiar, I believe you're good.
Thanks, if that's the only place that the limitation comes up, then I'd say that you can have both.
This ability does not allow you to have both a familiar and a bonded item.
That's no where near open enough to imply a global limitation.
Just to make sure its understood, the Arcane Object from the Eccleiathurge archetype is only going to affect the cleric spells memorized. It will not act as a Wizard's bonded object and will not have any effect on the Mystic Theurge's arcane spells.
Not sure if that was just unfortunate phrasing or a mistake, but it does act as the Wizard's bonded object, except where specified otherwise in the ability.
functions identically to a wizard’s bonded object except it can be used to cast cleric and domain spells (instead of wizard spells) and the ecclesitheurge can grant his bonded holy symbol only magic abilities appropriate for a holy symbol or a neck slot item.
Now as for how that interacts with a prestige class, if that's what you were referring to, then it's a little weird. I think the intention would be for it to only let you cast the highest level spell you'd be able to cast as just the base class. But I'm not sure if the RAW backs that up.
https://paizo.com/paizo/faq/v5748nruor1fn#v5748eaic9nii
Witch: If I take levels in a prestige class that advances my spellcasting, do I continue to gain bonus spells from my patron as I gain levels?
No. That is a class feature of the witch class, and the standard "+1 level of spellcasting" prestige class ability only advances spells known, spells per day, effective spellcaster level. (You retain the patron spells from your familiar based on your actual witch level, of course.)
This ruling is the closest thing I could find to this issue.
Edit: You may have been meaning to say that you cannot use the cleric ability to cast wizard spells. In that case, yes, the ability is very explicit that it's cleric and domain spells only.
Most things that give Arcane Bond or Familiars refer to them as equivalent to a Wizard's. This means the class levels stack and you only get one. There are a few ways (very few) to get more than one, but I don't know them.
/cevah