Yes, the "winding length" is what you've got to watch out for. One thing I found out on my Fender American Standard jazz bass in regards to winding length....when you install the E string THRU THE BODY you are displacing the string by approximatley .900 further back towards the bridge vs top loading it.
I'll try to explain this. If you want to know how the end of the winding length will "fit" at the tuner and nut when going thru the body....take the new E string and install it thru the back of the bridge as if top loading....but don't wind it around the tuner. Make note of where the winding length ends at the nut end of the string. Grab the ball end of the string and pull it back approximatley .900 (as if you were removing the string) and look where the winding length is at the nut. This will tell you what you need to know right away as to whether of not you have enough winding length for the string to work when going thru the body. I've saved myself a bit of grief by doing this.
The same applies to E strings that are tapered at the ball end. When I bought my American Standard Jazz, the factory installed Fender strings had a tapered E (thru the body) and it was a perfect fit. Because they worked so well I bought a new set of Fender strings...9250's as listed on Fenders website....only to find out they had changed the strings. The tapered end was shorter, so when I tried intalling the E thru the body it didn't work. This is when I started taking measurements and found the .900 differance when going thru the body vs top loading.
I sure hope this makes sense to all of you.