How to prevent watery spaghetti squash
One simple change you could make is to simply not mix the squash with the sauce, instead, plate the squash and then pour sauce over the top, the sauce will cool quicker which will reduce the amount that the squash cooks past the point you decided that it was ready.

If the squash still cooks too much on the plate, try starting your sauce earlier and letting it cool so it's warm but not scalding when served.

I wouldn't recommend just taking the squash out before it's done and letting it finish in the sauce, since as it's cooking, it releases water, which would be lost in the oven, but would thin the sauce if it's cooking in the sauce pan.

If you need mix it with the sauce before serving, let the sauce cool to the point where it won't cook the squash further before doing so.