The correct answer is, determine the CR/challenge you want to have for the fight and then set it up to be that challenge.
Ignore how or why the creatures are there, if they are there at the beginning of combat they are part of the CR. If they are summoned in after combat has started they aren't (because of the time/actions spent in combat to bring them come from someone else, they're effectively part of another characters CR).
Follow your orders is not necessarily a reasonable task. You would need to give it more specific orders, the other is too open ended.
Technically only summoned creatures are prevented from summoning more creatures. Called creature can technically call more. But again, this feeds into the CR of the encounter. And you should have already set what you want the CR to be. So sure, you can have the called creatures call more creatures but they will count against your total CR allotment.
Treat inherent bonuses as a bump in the CR of the creature, depending on how much the increase actually affects the creature. If you only increase the stat by 2 (or modifier by 1) then it's not a full CR step, but maybe increasing 4 creatures by that is worth an counting 1 creature as 1 CR higher (because we don't have CR 4.25).
Edit: Just realized this was about guidelines for the player not about handling running an NPC conjurer.
As a GM I'm not that friendly towards PC conjurers. I tell everyone at the table they can only have one permanent active minion. Whether it be a animal companion, familiar, called creatures, undead. More than that slows down the table too much, and is unfun for other players. Summons are required to have their stats written down on an index card, and if multiple summons are used other players get to run other creatures so your individual turn doesn't take so long.
As for the "obey me" command. Doesn't work. Each specific subsequent command given is evaluated for "reasonability".
I'm not so sure that "follow my orders" is entirely reasonable. Why would you give any other task if that was reasonable? It encompasses everything, and it can include many tasks.
The general way to deal with chain binding genies and the players getting too many wishes is to send genie hit squads against them. Which is something I imagine genies would really do.
Being as powerful as they are, they wouldn't take lightly people abducting them for wishes. You could set a precedent that it's okay to bind and kill genie-kind otherwise.
The alternative is that they also keep a humanoid around in their settlements so that he can "wish" to undo the wishes of other people that abduct or otherwise abuse genie-kind. He would otherwise be well kept and having to do no other work.
Basically no matter what you do, don't let players abuse wishes or get to many of them, just as you wouldn't abuse them against the players.
Main point to remember: don't allow bound efreet to grant wishes. At all. Or you will probably regret it.
Freeing a genie from someone else’s binding, on the other hand, should get them a wish in gratitude.
Both, comes down to the players, the party, the wish, and the story.
Allowing wish granting still allows room for the wish to fail, be perverted et al.
Is a bound genie casting wish something that most DMs who play at high levels allow or not?
In general, not allowed. At best, I will allow them to free a bound genie and get a wish as a reward. But I keep wishes scare or they become highly abused.