H100 is easier to mount on the air 540 since it's made with liquid cooling in mind.
however, h100 won't out perform a top end air cooler like a phantek/silver arrow/DH14 by much especially if you pair it with a superior airflow design like the FT02/RV02. when considering the performance of any cooling, you need to take into consideration the decibel level of the solution so that you are comparing apples to apples. you CAN use a hyper212 and have it perform almost as well as a top end cooler if you put a pair of 300CFM delta fans on it
but... it will be ear bleeding loud
so the question is would a H100 perform as well as a phantek at the same decibel level? the answer is no. liquid cooler can't be as quiet as a high performance air cooler because at the very least, there is the water pump noise you have to account for.
the question you should ask yourself is do you feel you'll ever go full custom liquid somewhere down the road? if the answer is yes, then go with the air 540 since it's obviously made with liquid cooling in mind.
however if you are willing to do a fair bit of modding. the FT02/RV02 is still the better solution since it can use a 540mm rad (3x180mm) internally. I'll let this picture do the explaining as to why i say it's a superior solution
and yes the one in the front is your standard 360 rad (3x120mm)
and MOST people consider a 360 rad to be a big rad
you can imagine what a 240 rad (H100i) looks like by removing the length of 1x120mm from the 3x120mm rad in the picture
remember. buying a high quality case is a decade long commitment. so don't simply think about your current build, but future builds as well. a high quality case should last you AT LEAST 10 years if not longer. the ONLY reason to replace a well designed high quality case is you eventually got sick and tired of looking at the same case every single day for over 10 years
or your taste has changed and wanted to go with a smaller/quieter machine. it's the main reason i spent the extra $ to buy the FT02 instead of the RV02 because the elegant look on the FT02 is timeless. i doubt I'll ever get tired of looking at that case as time goes on and it's quiet enough for bedroom use when paired with a fan controller.
so.. if i were to buy another case in the future, it'll definitely be a SFF case for a HTPC. it definitely wont be because the FT02 cant accommodate whatever hardware they can build for the consumer market.