regarding the new toll fee application sa NLEX that started July 1, cars with topload that exceed 7-feet will be the ones charged with class 2 fees. so i dont think bike racks on the roof will count as C2 as far as sedans go, but if you place your bike already then prepare to shell out extra. i'm not so sure about AUVS, SUVs with topload.
as for the topload registration, additional P100 payable (regardless of the topload configuration or contraption whatever) to be added and co-terminus with the car's LTO registration. its better for you to include it with the registration month, if you do the topload reg after it'll be more costly with the comptuer fee the LTO charges.