DP, I still don't get it.
When I depart from Rotterdam, or arrive there, I just put in, say, Mike as the entry/exit point of the CTR. From there it's DCT to or from the field. At least, that's how I load up the GPS. I know the route between the field and Mike is not DCT, but I typically can't be bothered to put the whole route in - especially when the official route is curved because it follows a road, river or railway.
If the GPS I'm using shows VRPs (e.g. SkyDemon) I really don't have to reprogram the GPS to fly to a VRP if required. I just glance at the GPS, find the VRP, look at the approximate course I need to fly, set that course and see what happens. And if the GPS doesn't show VRPs (e.g. GNS430) I typically set the zoom and declutter level so that I can see the whole shape of the CTR, preferably with some major roads or rivers visible. I then use this overall shape and the aircraft symbol to look at the Visual Approach Plate on my lap, and can identify where I am on that VAC with an accuracy of less than a mile. So I can still fly to a VRP anyway.
In fact, I would probably prefer the GPS to accept a route starting at the VRP at the CTR boundary for my departure airfield, and ending at the VRP on the CTR boundary for my destination airfield, so the screen doesn't clutter up my departure and arrival. But somehow GPSs seem to be confused by that concept.
In any case, the aircraft doesn't fall out of the sky when you deviate from the magenta line. So if the magenta line shows DCT, but you have to dogleg via a VRP, just use the overall shape of what the GPS screen shows (including the DCT leg) and the GPS screen or paper VAC to fly to that VRP. I don't see a need to update your route in the GPS to actually show the dogleg via the VRP.
And consider this: Pre-GPS, did you draw your exact route on your map or VAC as required, with heading, timings and such? CTRs only have an 8-mile radius. That's four or five minutes flying time in the average spamcan. If you can't navigate visually for five minutes, then what?