"Please note that Game A, DLC X and DLC Y are included in Game A: GOTY Edition but you already own these items, and will not receive another copy when you buy this pack." If the system is able to warn me at checkout that I already own something, why can't it mark those entries as owned to begin with?

I own all the content included in the following entries that are not marked as owned:

https://www.gog.com/game/age_of_wonders_3_deluxe_edition
https://www.gog.com/game/divinity_original_sin_enhanced_edition_collectors_edition
https://www.gog.com/game/dont_starve_alone_pack
https://www.gog.com/game/evoland_2_deluxe_edition
https://www.gog.com/game/fallen_enchantress_legendary_heroes
https://www.gog.com/game/fallen_enchantress_upgrade_to_ultimate
https://www.gog.com/game/gods_will_be_watching_special_edition
https://www.gog.com/game/guild_of_dungeoneering_deluxe_ice_cream_edition
https://www.gog.com/game/hybrid_wars_deluxe_edition
https://www.gog.com/game/kyn_deluxe_edition
https://www.gog.com/game/last_federation_collection_the
https://www.gog.com/game/master_of_orion_collectors_edition_upgrade
https://www.gog.com/game/not_a_hero_global_megalord_edition
https://www.gog.com/game/pathologic_classic_hd
https://www.gog.com/game/pillars_of_eternity_champion_edition
https://www.gog.com/game/pillars_of_eternity_hero_edition
https://www.gog.com/game/pillars_of_eternity_royal_edition
https://www.gog.com/game/pillars_of_eternity_the_white_march_part_1
https://www.gog.com/game/pillars_of_eternity_the_white_march_part_2
https://www.gog.com/game/renowned_explorers_bundle
https://www.gog.com/game/shadow_warrior
https://www.gog.com/game/shadow_warrior_2_deluxe
https://www.gog.com/game/shadowrun_hong_kong_extended_edition_deluxe
https://www.gog.com/game/the_real_texas_dusty_skies_edition
https://www.gog.com/game/tropico_5_complete_collection
https://www.gog.com/game/valhalla_hills_twohorned_helmet_edition_upgrade
https://www.gog.com/game/wasteland_2_directors_cut_digital_classic_edition
https://www.gog.com/game/the_witcher_3_wild_hunt_game_of_the_year_edition
https://www.gog.com/game/x_rebirth_home_of_light_complete_edition_upgrade

I have accidentally bought Cities in Motion and then the Collection upgarde, yet I don't seem to own the Cities in Motion Collection.

because GOG's system socks horribly, maybe. I have several games that don't show as owned, and/or don't get update notices. There is no correlation. Some games not marked as owned do get update notifications, others that are marked don't. And GOG doesn't give a damn either. These problems have been here for YEARS.

Speculation on my part, but it could be that while you own the very same files, the entries are different.
Let's take a fictional example of game X, which you can either buy the Collector's Edition or the base game plus the collector's upgrade. The collector's upgrade includes just the soundtrack for said game.
If you purchase the Collector's Edition, GOG will give the cut to the game's publisher. If you buy the game and upgrade items, GOG will give the game's cut to the game's publisher, but the upgrade's cut to the soundtrack's composer. So even though in both cases you get the same end product (base game plus soundtrack), for logistical reasons GOG has to keep the products separate.
Similar thoughts can be applied to kickstarter editions (how many keys should we expect to give in the future), retail activations, pre-orders for games etc.

As I said though, plain speculation on my part. Don't know if that's really the reason GOG did it, or if they have a different reason for doing so.

Hmmm this reminds me of SotS when getting The Pit, then getting the expansions later which effectively gave you the gold edition (and even gave you an upgrade package download) but the gold edition was still an option to buy...