Edit: apparently you can gain favor for money, but that's only during the morning.
No, the option to give her money remains throughout, at any time of day (certainly in the evenings). She'll only stop intercepting you to
demand money.
Wrong. I had roughly 300 Favor at the time
If you keep spending you favor points—especially if you have, for whatever reason, been stingy about handing over gold to Irith along the way—you may not have a lot in the bank, but it doesn't change the fact that at this point, having paid back the Guild and with Nyx working for you, you should be very close to earning gold more rapidly than you can spend it.
You'll run out of available favors well before the endgame, anyway. Your poor downpayment strategy only leads to the scenes being more spread out than they would otherwise be.
It's still a huge amount of favor loss due to a bug
Just because it didn't work as you expected, that doesn't make it a bug. And if you're about to do something major like handing over 75K in gold, you ought to save first in case, precisely because there might be unexpected complications. (Or, you know, just rewind afterwards.)
Or the walkthrough might be interpreted as doing 5 days of cage will give you +5 all at once. Unless you're telling me the you want the game to continue to give vague and unintuitive instructions, there's no argument to made here
In-game hints
should be subtle, yes.
Now, the walkthrough is a different matter.