EAC does not update syscfg.xml(at least not the last version I saw). You update syscfg.xml, and then restart EAC to get it to pick up the changes. Or you can just install all the cobol components to something like /opt/svrexp2.2 or whatever is in syscfg.xml to get around the problem in the first place.
Mincom recommends using a different app server and developer server because apparently the app server is more efficient in its use of licenses. I have no idea if this is the case or not, and I generally just install it into one place to make keeping track of the licenses simpler(you get difficult to track down error messages if your app server licenses are installed in the developer cobol, and you are subscribed to the appserver cobol - remember this to prevent heartache if you use two different locations). Haven't run into any real problems with clients who have gone into production this way, but it would be interesting to see a benchmark and find out what is really happening.
I haven't ever been on a Tru64 system, so I have no firsthand experience there. However, on HP-UX 11i 64 bit Server Express causes the cobol programs to fail. If you can successfully run something like mimsrts MSB000 then you do not have the same problem.