I believe she did take them apart and swap parts, as the article said she demonstrated the hans-on method in court.
I must have missed that part. If so, then yes, she "customized" them.
Still, I can't stop thinking that Geobra just wants to give sellers a scare. Specially what I call the "large scale private sellers" that are not Geobra sanctioned retailers.
And about the themes of the customization, I totally understand and
agree with Geobra that going religious in the themes is very iffy. Some passages of the Bible or Koran could be deemed offensive to some Christians and Muslims, and PM being an innocent toy, it has no business meddling with that. Yeah, yeah, I know better and you all here know better, but some people might take offense. So Geobra is very wise in keeping distance from these subjects.
The nativity theme is a bit different, since Christmas has been universally accepted in the modern world, so Geobra "can" issue sets in that theme without fear of getting a large bunch of people upset.