Sounds like the district CFO has some experience with this with other PTOs in your area, so his advice is probably the best. I'm guessing that he has a group exemption set up, where all he needs to do is file your tax ID number with the IRS, and you'll automatically fall under the district's exemption. He's also right in that you will still need to file your own 990 if your gross receipts exceed $25k (no getting around that one...).
The thing I would be concerned about is the requirement that you keep the funds in a "school account." I'd get some more details from him on that in terms of what kind of control you would have over the money vs. what kind the district would have. There is probably some sort of agreement that would need to be signed between the PTO and the school district that would spell all this out.
Can you call other PTOs in the district and find out how the arrangement works from their perspective? If they have had any problems with it? If they are run significantly different from your PTO? If what they tell you is something you can live with, falling under the district's umbrella is probably your best option.
If you don't want to go that way, though, at least the filing for exemption is a one time event! Once you get through it, you'll never have to do it again.