!142 (merged) had no respective discussion of whether or not to use a different subdir. So chance is this was just subject to general 5->6 changes.
As suggested n https://phabricator.kde.org/T16161 there might not be a reason respective to the change of using Qt6/KF6 instead of Qt5/KF5 here. As there is no change in the data format itself, only the library using it changed ABI :)
And changing the subdir also requires (for quality user experience) to implement migration of the user configuration, to not leave behind dead config files in the old subdirs and instead defaulting the UI to user's frustration.
Still to be solved is support of plugins which might want to support being installed in parallel. How is this solved for other configuration data of plugins?
Edit: Than there is https://phabricator.kde.org/T12409 which proposes to "Move kxmlgui files from GenericDataLocation to ConfigLocation". To which I agree. So a more complete solution would be to have someone implementing support for that instead, including some KXmlGui5Migration class (similar to KDELibs5Migration. Until then IMHO KDEInstallDirs6 should keep using the old kxmlgui5 value.