Sorry for not keeping up here--remember if you need to get ahold of me I'm just an email away.
There are slight modifications. Adding support for aftermarket panel attachment so you can lasercut your own panels and not have to drill and tap the frame. Also per customer request widening the c8 cutout to support c5 jacks. The big change is fixing the skyslot pattern to be VESA compatible again. There was an error with the die setup and it made all of us really sad. Could have been a really expensive fix, but it needed to be right.
I think what you are describing is that the heatsink actually goes up to the shroud, so you can't install noctua slim fans over it. Many GPUs are like this, all the single fan GPUS I can think of right now off the top of my head actually.
The SkyBracket Duo was made per customer request...sorta. With the S4M-C users like
@Reldey removed the shroud and fans from their Zotac cards and used zipties to attach them which in theory would apply more pressure to the heatsink than a single slim 120 fan as I proposed before. It was a good idea, so I incorporated it--however it is NOT a universally supported feature or anything. It's just a drive bracket that can allow you to use these fans in certain configurations. For YOUR gpu, the fins are parallel with the length of the GPU, not transverse, so you actually wouldn't want to use the Skybracket Duo for mounting two fans even if you could because they would fight each other for pressure.
So I would stick with your original fan, or if you really want to replace it with something else, remove it and cutout a fan from it's frame and attach it that way. Sorta like Untero from my Discord did with his GB card:
BTW a link to my discord:
https://discord.gg/Mz7CfD
The new revision of the S4M (going on sale soon) supports this. I don't have pictures except for something like this: