I frequently see strange things. For example a form or program script that stands only in the B40U_c4_stnd. The object (runtime path) stands also in the B40U_c4_ags0 directory! I thought that if a form or program script was applicable in another VRC too, the entries in the tools tables should also be present. So not only on runtime level.
I see for example in a solution that a program script is updated in three VRC's. The objects are indeed updated in three VRC's. But if I look in 'Maintain program scripts' (or in table ttadv230) I only have an entry for the B40U_c4_stnd. Is this normal behaviour?

Yes, this is normal behavior. It means that the object is created from the source in another VRC. This happens when the script source is the same, but one or more used functions (includes) are in the object VRC. You can see in ttadv2539m000 which objects are created from which source.