How to disable only some Windows 10 global shortuts to use them in third-party applications?

You could use Autohotkey for remap any hotkey to send another hotkey using Send command:

#k::
Send {WIN up}
Send {k up}
Send ^+p
return

After this pressing Win+K will send a Ctrl+Shift+P which will show Command Palette in Sublime Text, you can use this way to override any hotkey to send another hotkey, set it to something like Ctrl+Shift+F3 and assign that hotkey to Sublime Text's paste(in keybindings) and then use Win+K to send that Ctrl+Shift+F3 to Sublime Text which will call paste.

AutoHotkey script:

#k::
Send {WIN up}
Send {K up}
Send !^+{F3}
return

Sublime Text keybindings:

{ "keys": ["ctrl+alt+shift+f3"], "command": "paste" }

Edit:

Seen your Please, don't offer AutoHotkey shortcuts redirect to other shortcuts. why not? Above example works even for Win+R:

#r::
Send {WIN up}
Send {r up}
Send !^+{F3}
return

Text successfully pasted through Win+R in Sublime Text.

Edit 2:

If you really like to assign real hotkeys you could disable all Win+{KEY} hotkeys, and then create your hotkeys which will do same as default Win+{Key} hotkeys, and for another hotkeys assign your own actions.

For example for Win+R:

explorer.exe Shell:::{2559a1f3-21d7-11d4-bdaf-00c04f60b9f0}

Works, but for some hotkey its hard to find how to call their actions.