Upgrades are tempting. I've enjoyed your posts on the super so far, so I thought I would quit lurking and chime in.
My super has the round porting holes and it seems to work as well as any of my other flash suppressors. Out of 5 different .308 rifles I own, only the FNAR has lighter recoil than my VEPR Super, so I don't feel the need to try and reinvent the wheel on that part. Best solution to lighten it up a bit may be to try some 7.62x51mm NATO rounds through it and see if you like that better as they tend to feel lighter to me than .308 even though they are interchangeable in most 308 win rifles.
You will most likely have to cut off the ported area in order to change to a different flash hider or suppressor. I am picking up a 16" version 01 for playing with those type of modifications since chopping up the super is not to my liking.
The twist ratio is what it is and I will have to spend more time with it at longer distances to know how I feel about that, but it is going to stay as is for me as that would also require major disassembly to change.
I am totally with you on the stock. It is pretty and also kind of soft, so I don't want to take it out and risk banging it up in the woods. Something much lighter with a cheek riser would be very nice as well, but I am fine with the LOP as a fairly tall guy a little over 6'.
I think we may very well be stuck with the super as is for a while as they don't seem to be a high volume item. Low demand makes for even lower aftermarket demand.
The top mount seems to work better for me by switching over the locking lever to be on the left side where it can lock down on the upper notch that does not exist on the right side, almost like it was designed that way. It also doesn't seem to loosen that way as it is torqueing the screw as you push it down. I'm not sure why it shipped put together backwards, but it is easy enough to fix. It may not help with scope clearance, but it helped keep the charging handle area unobstructed for my big mitts.