Yes, you have to plan a VFR flight on the basis of not getting a CAS transit, but there is no conflict between that, and planning via navaids and airways intersections.
Unless of course you can't find any of the above where you need to go... then you have to stick in a user waypoint, and for that I use the VOR notation. I have never used lat/long, in 6 years of flying. Much too error-prone, for a start.
Personally, once outside the UK (but not Italy which can be as anally retentive as the UK), I tend to plan a navaid-based route that I actually want to fly, and the fallback (no CAS transit) plan can be quite messy and I don't mind flying the resulting doglegs with the GPS. A bit tacky but OK if you have good clear maps on the GPS.
That was before the IR; now I don't bother with any of that VFR stuff when going abroad, and just fly on at FL150... Navbox isn't good for IFR/airways; one needs something into which one can stuff the airways route and it generates the plog with all the waypoints that can be loaded into the GPS.
The jury is still out on the N-reg issues I am afraid; the DfT minister is supposedly going to make a decision on it this year sometime. God knows what they are going to do... the mind boggles. Whatever they do, it will be as logical as the CAA simply invoicing every N-reg owner with £23.45 every year