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I think I see the problem. The Green Faith Marshal's "Power of Nature" ability alters the Inquisitor's Domain ability. The normal ability gives you the Domain Powers but not the spells. The alteration gives you up to 6th level spells. While it does not explicitly say it removes the Domain Ability (the Familiar in this case), it can be read that way. It can also be read as adding the spells (as the Stern Gaze ability of the Inquisitor is also replaced in the process).
For a case like that, you may need to search the Paizo boards for an official ruling on which way it should be read (which you are unlikely to find as official rules corrections/clarifications for Player Companions are very very rare). You can also raise a bug report regarding the implementation based on it adding the spells instead of replacing the Domain Ability with the spells... but as an obscure case, it may take a while to get any attention.
As for whether having more than 1 companion is a drawback.. I wonder if you mean something HeroLab doesn't support? The fact that you found a work-around means it is supported... but you may be "on your own" if you multi-class in a way that would cause unusual stacking, for example, and they don't seem to work as expected.
As a test case, I added level 6 character with 3 Druid levels and an Animal Companion, plus 3 levels of Sorcerer with a Familiar, and then bought a Mount. All three "minion creatures" appear in HeroLab normally, so I think your issue really is with the way the Green Faith Marshal's "Power of Nature" has been implemented.
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