Item progression works for every upgrade when EnableRandomizeUpgrades is active

[tixomirof]

With Enable Randomize Upgrades = true, it does not matter which upgrades you have in lategame store list, if you sell items for item progression, it will apply to all upgrades in the mod.

Other config options from randomize upgrades category:

[_Randomize Upgrades_]

## Upgrades will be randomized per selected event to be allowed purchased on the store.
# Setting type: Boolean
# Default value: false
Enable Randomize Upgrades = true

## Amount of Upgrades that will always appear in the store (if allowed).
# Setting type: Int32
# Default value: 5
Amount of Upgrades = 10

## Wether purchased upgrades will always show in the store and the specified amount of random upgrades will not include these in the selection.
# Setting type: Boolean
# Default value: true
Show purchased upgrades = false

## Event which triggers the random upgrades being changed in the store.
# Setting type: RandomizeUpgradeEvents
# Default value: PerQuota
# Acceptable values: PerQuota, PerMoonRouting, PerMoonLanding
Randomize Upgrades Event = PerQuota

Ex: you have only running shoes in lategame store. Tattered metal sheet contributes to running shoes and back muscles. Upon selling tattered metal sheet, it will give points both to running shoes and back muscles. But expected to give only for running shoes.

[WhiteSpike]

So you wish item progression to not affect upgrades hidden from randomize? The two systems were made without considering each other thus why you are describing this.

[tixomirof]

So you wish item progression to not affect upgrades hidden from randomize?

Yeah, exactly, if that's not a problem, of course