Are you sure they are both 5k valves? If your ram BOP is 10k, and the valve on the choke manifold is upstream of the choke, then it will be a 10k valve. If the valve is downstream of the choke then it will most likely be 5k - note that there is nothing written in any standard that says that valves downstream of the choke can be one pressure rating lower than your ram BOP, but that is how rigs have been built as long as anyone can remember (I realise that I may be telling you something you already know, so apologies if I am).
There are five pressure ratings (2M, 3M, 5M, 10M and 15M) for an API 4-1/16" flange, so you may have to check the flange size etc to be sure of the actual flange rating.
There are a couple of internet sites that you can access an electronic version of a flange 'slide rule'. Here are a couple of sites from Claxton (Great Yarmouth, UK) and Woodco (Texas, US of A).http://www.flangesliderule.com/http://www.woodcousa.com/flange/slidemenu.htm
If there is some uncertainty about the flange ratings, these sites will help you identify the flange (even if the flanges are made up).
I sent Woodco an email a couple of years ago and they very kindly sent me a few 'hard copies' of the their flange slide rule for when you don't have internet access. I think Claxton would also send you a hard copy if you asked them.
The only other difference between a 4-1/16" 5k flange on the standpipe or choke manifold might be that the flange on the choke manifold may be dressed with a pressure energised ring gasket (RX-39) and the same flange on the standpipe may be dressed with a standard ring gasket (R-39). The flange faces on an 'R' type ring gasket will have a larger gap.