This thread is quite old, but I though it may still be useful to reply here 
The lenses are the same, just different mounts. The Pro version is fixed mounted into Novoflex’s bellow adapter, so you cannot remove it (I own that one too) while the Flex version requires the screw mount plate to be attached to the bellow system.
The SK APO 90mm lens is great, while not specifically made for 1:1 repro, it still performs well on that scale (stopped down to f/7.1 - f/8). Though I’d advice to purchase a different lens from the Schneider series with better results and at a lower price (used), if you plan to use it for film scanning only. Look out for the Schneider Kreuznach Makro Symmar 120mm f/5.6 – It’s available optimised for different magnifactions. Depending on which camera sensor size you use (APS-C, FF, Medium Format) you may want to go for the 0059 (1:1.33) or 0058 (1:1) version.
This is the full list of available versions:
SK Macro Symmar 120:
- Version 0058/0158 | Optimised magnification: 1:1
- Version 0059/0159 | Optimised magnification: 1:1.33
- Version 0060/0160 | Optimised magnification: 1:2
- Version 0061/0161 | Optimised magnification: 1:3
SK offers the lenses in both consumer and industrial versions. The industrial one is widely available on the used market for prices ~ $400-$500. The difference from consumer to industrial are missing aperture clicks on the latter and also the aperture is numbered 1-6 instead of the aperture value.
A small warning here though: 120mm for film scanning @ f/5.6 gives a thin depth of field, so you need to make sure your film is really flat for best results.
If you wish to use a less painful DoF, look out for the Rodenstock APO Rodagon 75mm 2x f/4.5. I strongly advice to go for the 2x version here, as the 1x version covers only up to 6x6 MF negatives while the 2x version has a super huge image circle and performs better in magnifications other than 1:1.
I own all lenses mentioned here (and also the Novoflex BALPRO bellow system), so can speak from experience – In case that matters
Both the SK120 and R75 have a M39 mount, so they can easily be used with Novoflex’s bellow system and the L39 mount plate (both in reverse and normal mount).
Happy to answer questions, if any.