The logic is that the European version is the parent, as in MAME. If not available, the US version is the parent.
what you experience is a problem related to the fact that lists are not split by region [*], and this is on purpose: as the lockout message explains the program is compatible with both regions and it checks not to be run in the wrong country.
you can use list of favorites to sort regions (e.g. filtering out games with USA/Jpn in the description for PAL systems and Euro games in NTSC systems), but hardware-wise there is no reason to split the software lists by region
[*] exceptions are made when the game data are not compatible across the regions, like for PC-Engine vs TurboGrafx (wrong region = black screen, because of different byte order in the chips inside the carts), or like for MegaCD vs SegaCD (wrong region = CD detected as audio CD)
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