Hi ellgey -
There's a couple of independent, though related, ideas here. I'm not a lawyer, so my analysis of nonprofit law is not Gospel by any means, but I can jump in on some "best practices" issues.
More or less, I think you can donate your PTA funds to your school and be OK. The larger question is: do you want the school to control your funds? Typically, my answer to that question is: "No."
In your case, it may be an easy solution for what to do witht he funds in your PTA account before you dissolve, especially if the school and your group have a basic agreement on what the funds should be used for. Know, though, that once you donate the funds, they can be used anyway the school sees fit. The super could come in the next day and take those funds for the general school budget.
Same holds true for your PTO funds and using school ID numbers for your PTO. There's some real questions about whether what your bookkeeper says is true (I suspect IRS would say no, though i haven't seen a ruling.). But more importantly, I think there are real advantages for PTOs setting up as independent. I can't tell you how many emails I get from groups where Principals or districts are controlling the PTO or PTA. True legal and financial independence helps (a lot) in that situation.
Creating a strong, independent PTO is better in the long-run for involvement. As long as you are running your funds through the school and operating as a legal non-entity, you have no legs to stand on if/when there are any issues between you and (for example) a new principal, etc.
In a nutshell, I think there's a strong chance your bookkeeper is wrong technically. And, more importantly, I think going that route is the wrong way practically even if it's OK technically.
My $0.02