Those HPLC columns can be used with pure water

You should be asking about reversed-phase columns, because it is commonplace for gel filtration to use a pure water phase.

Agilent's Bonus series, and Aichorm's Aqua series, are all capable of pure aqueous phases.

But if you just consider the high aqueous phase ratio at the beginning of the gradient, it is not necessary, ordinary C18, C8 can be flushed with pure aqueous phase for a short period of time, no more than 10 column volumes, it is not a problem.