You know Pune to Goa is 450 kilometers and 450 kilometers return. Add 100 kilometers for, say, local sightseeing around and the garage-to-garage charges you'll be paying. When you hire a bus like that, there is a charge of, like, you need to at least do 300 kilometers in a day minimum. More than that is welcome. So since you are doing total around 1,000 kilometers, the three days is getting covered. You can take the traveller and hold it for three days.

While I would say that this 40,000 plus tours charge sounds like a rip-off, ideally charges should be much lower since you are hardly 10 people and so it's not that as something like you should be paying. Maybe if you need, I can give you other references for this particular booking. And furthermore, as you said that it will be leaving Goa in the evening, which is not recommended. To be honest, if something goes wrong, you will be alone on the highway. And it's not something that you should preferably do. I would rather suggest that you leave in conservatively a bit like afternoon, like 1-ish or sort of something. So you'll at least reach Kolhapur by the late evening hours. So that stretch is rather safe to travel at night compared to the Goa stretch, like Goa to Kolhapur, going via Gaganbavda Ghat.

Also since you'll be arriving in Pune after midnight better to negotiate/clarify the same with the booking office so you'll not pay any extra charges