However, in early game you obviously have to dump every single skill point for your digger into hard digging traits, so no supply skill for you. Besides that, if you want to use the morale boost for a desired skill, going digging-building-supply is painful, and you'll still want your builder to take operating too later on.

And that's where we disagree. In the early game, yes, you definitely want to take the first Digging skill, but you likely won't have an immediate use for the second or third for quite a while. I rarely touch my first Abyssalite tile until after cycle 40 or so, by which point I can select the second-tier Digging skill as the Dupe's fifth or sixth skill.

Supply skills make an obvious second skill and possibly third for exactly the reasons you've stated above. Digging-building-supply is hardly painful unless you unnecessarily max all the skill paths right away. Now, the bit about giving this Dupe Operate as well - I typically use other Dupes for Construct + Operate.