So far as I can see, neither the GEDCOM 5.5 nor 5.5.1 specifications have an item that enables one to record which given name is actually used in normal life. That suggests that, with no target to aim for, each program may very well have its own conventions. The software I use, for instance (Family Historian from Calico Pie), has an item "Given Name used" so that where the given name is "Charles Edward", then I can enter "Edward" into "Given Name used". I then print that GNU in brackets (after the full name) in charts. The "Edward" goes into an extension tag on the GEDCOM file, thus:
2 _USED Edward
But that's just what they (and I) do.
I'm sure that I've seen Tony Proctor's underlining used elsewhere but this may tend to be a hand-written thing.
The only other thing is to point out that this is also a real life problem - I think that for English & Welsh probate purposes the request is that this sort of thing is done by supplying multiple names - so if "Charles Edward XXXX" were known as "Edward XXXX" in daily life, then both (full) names should be supplied and the calendar would refer to
"Charles Edward XXXX" also known as "Edward XXXX"
Another thing is to remember that each software displays stuff differently so that what works in one, may not work well in another - Ancestry's on-line trees have alternate names but it's not easy to see that they exist, never mind what the values are.
So - you pays your money and you takes your choice....