Welcome to the site !!
From what info I just gathered on Honda's website , they seem to be the same basic bike/frame , the only listed differences I found was suspension length was longer on the Rally , and the obvious add-ons , so with that info , I would say they are the same frame and yes the skid plate should work
Can I ask what your reason for removing the bottom fairing was for ??? , easier maintenance ?? , as i would think the purpose to get the Rally over the base L would be because of the "Dakar look" of the fairings , etc , since otherwise in performance (minus suspension differences) they are the same bike but at a higher price because of the fairing and add-ons , so removing it to me seems to defeat the purpose of buying the more expensive model .....