Hello T3CC,
to the best of my knowledge, the only to "upgrade" from one edition to the next would, unfortunately, be to purchase the Definitive edition outright.
If you were to look in your library at a game you own above the 'standard' edition, you will see that it is listed as the base game, with the additional goodies being listed under Extras or DLC as appropriate. Despite this, the store treats two different game versions distinctly; as separate entries. Thus, a "deluxe upgrade" (such as
this one, for Shadow Warrior 2) is required to bridge the gap; to add those missing extras onto the base entry in one's library.
The fault lies not with one entity, GOG or a given publisher, but a little of both: GOG presumably doesn't have permission to throw up new store entries on the behalf of the publisher, but GOG still retains this clunky and annoying foundation that could do with a bit of automation and modernising.
Here are a couple of additional threads from around and about, just to demonstrate that this has been on ongoing issue:
https://forums.obsidian.net/topic/91454-pillars-of-eternity-edition-upgrades-on-gogcom/
https://www.gog.com/forum/pillars_of_eternity_series/option_to_upgrade_editions and not only for this game:
https://www.gog.com/forum/general/cant_upgrade_from_standard_to_deluxe_ultimate_edition If you already own the Hero edition, then you have the decision between purchasing the DLCs only, or the Definitive edition which includes the additional miscellaneous digital extras on top of that. The game and its extras are at a 75% discount at this very moment, so you may wish to ask yourself what is important: do you simply wish to own the
game expansions for a small fee, or that and the additional fluff for about twice that initial fee (depending on regional pricing): Perhaps. They are enjoyable niceties, but personally I would rather just purchase another game, instead.
There are also these threads:
https://www.reddit.com/r/GameDeals/comments/7d5x6b/comment/dpvzsgt/
https://www.gog.com/forum/general/upgrade_your_pillars_of_eternity_for_free that suggest it used to be possible to effectively obtain those additional goodies free of charge when owning the Hero Edition, White Marsh Expansion, and the Deadfire DLC, but I have no way of verifying if this is still possible (without spending money)