Ebay is obviously well aware that if they didn't charge the insertion fee based upon the "effective" starting price ie. the reserve price, that people would use the reserve price as a means of fee avoidance - they could set a high reserve along with a meaningless $0.99 starting price and only pay $0.20. Ebay certainly isn't going to let anyone get away with that!
PS - Personally I'm of the mind that Reserve price is a really bogus concept to begin with. Many bidders are turned off by them and the sell-through rates are miserably low on those types of auctions. If a seller needs to have a minimum price, why not just be up front about it and set a minimum starting bid and be done with it, instead of all the smoke and mirrors. IMHO