Monopolist, the Egyptians were already recruited in the Ptolemaic army and navy in very large numbers by the time the revolt broke out. You can only do so much with a small Greek population and constantly importing foreign mercenaries; they had to and they did use Egyptians in the Battle of Raphia.
I know that, I mentioned that in my post. If you're getting at where I said some sort of act like the one that let Egyptians get conscripted, well I meant something like it. I was listing off things that could help Hugronaphor's revolt take Alexandria... Lower Egypt and Alexandria are going to be hard conquests for him with just brute military force. 80% of the land doesn't mean 80% of the military and political power, obviously. Hugronaphor's going up against a more professional army, a much richer population, and not an overwhelming amount more people, if at all. He needs at least one of the things I mentioned to help him out (or foreign intervention...), I think - though I don't know what the act would be that could rally and militarize a lot of Egyptians to Hugronaphor's cause similarly to Ptolemy IV's arming of the Egyptians, I was saying something like that could help Hugronaphor.
Harmachis could carve a deal with Rome. Rome wanted Antiochus IV Epiphanes out because Egypt provided grain for Rome, no? Harmachis can make a deal with the Roman Republic recognizing him as Pharaoh of Egypt in exchange for military assistance against the Ptolemies and perhaps help defend them from Seleucid incursion via Palestine. It's not in Rome's interests to conquer the East yet, they were more than happy having vassals or allies handle the job.
OK, I said that Rome could either intervene before or after the Seleucids invaded; before meaning that it's taking place just long enough after the Second Punic War for Rome to feel that it's worth sending men to help the Egyptians fight back against the Seleucid invasion, and after meaning that it's taking place some point in the future after a successful Seleucid conquest, meaning another revolt entirely.
If Rome intervened before the Seleucids mobilized an invasion of Egypt ((which the Seleucids do in both scenarios that I'm talking about because Egypt appears very vulnerable and has always been a realm that Antiochus III and other Seleucids wanted to add to the empire) (after a successful rebellion... I'm assuming this is around the 195-190ish range)), and were successful (as I assumed they would be, which I think is reasonable enough) in fighting back against the Seleucids, they could do one of two options: do what you said and give Hugronaphor more or less complete autonomy, or they could make Hugronaphor a Roman puppet, like Pergamon and such. Annexing it would be incredibly stupid on Rome's part here; Rome would have to fight another war to fully pacify the Egyptians and somehow keep them pacified for a time afterwards... or they would have to come off as literally godlike liberators. Neither is probably going to happen. So, with the first two options, I'd say that Rome would likely go for the latter option... vassalization seems like the more appropriate, Roman-like thing to do, and probably smarter then merely recognizing Hugronaphor as Pharaoh and asking for a little more grain.
If Rome intervened in another rebellion, after allowing the Seleucids to take control (this is assuming a Seleucid conquest in like 200 BC (the conquest coming probably during the revolt rather then after like the other scenario...), which would probably require a Second Punic War PoD to make that war last a little longer... and I'm assuming again that Rome is victorious with the Egyptians), they could either 1) liberate the Egyptians and give them complete autonomy, 2) make Egypt a puppet of Rome, or 3) annex Egypt. Full liberation again probably isn't going to happen; Egypt's going to have to fight and win independence on it's own if it's getting full independence from Rome and the Seleucids. 2 and 3 depend on when this war is taking place; 2 probably happens if it's before 100 BCE; 3 still probably doesn't happen after 100 BCE, but is much more likely then before, assuming that this is more or less the Roman Empire that emerged IOTL.
So Rome in both scenarios I'd think would make Egypt a puppet. Hence my saying that Rome takes over; Rome controlling Egypt as a puppet means they do take over. And, making Egypt a puppet means that a more direct takeover is more likely, after all, Rome eventually took over the puppets that it had IOTL. Same thing here; Egypt probably gets annexed in the end if it's made a puppet. And, if Egypt manages to stay independent despite the Roman Empire's rise, ignoring as many butterflies as possible, Rome probably still ends up with Egypt in the end, as Egypt's a good place to conquer for a Roman general - but I doubt that Egypt manages to stay completely independent with these scenarios. But who knows, it's all butterflies.
I apologize, hopefully all I said is clear now; I've always been really horrible at explaining my thoughts with typing.