I think your plan will work. You saddlebags are molded of some kind of ABS or something, not fiberglass.
I'd install them in the saddle bag as prescribed in the instructions (with the provided velcro), coat the inside of the saddle bag with a good release agent and then lightly coat the inside of the liner and let it cure. Then remove the liner and add any additional layers.

 

Bingo.

I'm not 100% sure, but I think a good coat of hardened resin should hold the liner pretty firm until I can layer-up the inside. The fibers of the liner should absorb resin just like standard carpet I would assume.

If if works, this will be the best fitting sub enclosure I've ever made (and I've made lots). Never done one on a Harley though.