I have a custom SiteAccess-aware configuration that exposes, let's say, xx.yy config. Therefore, I set it like:

ibexa:
    system:
        site_group:
            xx:
                yy: 'abc' 

I can read value via ConfigResolver for all SiteAccesses belonging to site_group.

If I configure another setting, let's say native Ibexa's one for one of my specific SiteAccesses (beloning to site_group), the value of my custom attribute will be overwritten with null. For example (en belongs to site_group):

 ibexa:
    system:
        en:
            languages: [eng-GB]

With this configuration in place, ConfigResolver will return null for my xx.yy attribute even though it is set for the group and remained unchanged for specific SiteAccess.

It is reported as a bug as this has been working well in 4.3 and below.