Not sure what you're saying here...
Basically, that in many ways, Mouse could be seen as Harry's Minion. In several of the books Mouse appears to be semi-magic dog who does what Harry does him to. Harry sometimes wonders "Did Mouse think to do that on his own?" but basically treats Mouse as his dog.
Thomas can be seen as another of Harry's minions - at least in some books. He sends Thomas out to do things. He calls on Thomas' help in fights. He can count on Thomas to do more or less what he asks Thomas to do.
Neither of these appear on Harry's sheet. Not as minions, not as allies, not as Contacts - they are just people (okay, stretching that a bit for Mouse) that Harry knows who are there for him. If Harry wasn't charged for his minions (not even for Kincaid when Harry hired him) then why should the average PC be charged refresh, skill, milestones, etc for a minion?
In game time - that I can see. Harry has to walk Mouse, feed Mouse, see to Mouse's needs - and that takes up time in the books. Missing a scene or two to maintain a relationship - I can definitely see that. But I can't see charging refresh for companions, helpers, assistants, pets, etc.
Richard