For the kits. The lengths are the same. All the tubes are the same between the two versions.
The rollerball refill will go up into the finial which holds a spring to keep it advanced in the nib.
The fountain with a cartridge will stay in the barrel, but a piston pump will go up almost as far as the rollerball refill. remove the spring if it has one in the finial (got a Stateman Fountain that had a spring) to keep it from making a mess when you assemble/disassemble when inked.
As mike posted, if you are talking about a kit pen, then yes they will be the same length. If you are talking about a non-kit pen, then you can be just short or as long as you want.
Mark - I just didn't want you to think that you needed a blank that was long for a FP. I would say they look longer because of the nib and section gives it an elongated look.