I think they will stand out in a good way as well. I love the name Magdalena so much!
I think it would definitely stand out:)
It sounds like Madison/Madeline, but it stands out. Also, it has a ton of other nicknames other than Maddie (We have a surplus of Madisons in my area around my age- it's horrendous how many Maddies I know), from Maggie to Dali to Lena, and it's not a stretch for May or Meg. It sounds popular but it isn't. It's a flowery name that's historical and can be shortened into spunky nicknames.
I like Magdalena, but once I hear "correct" English pronunciation of this name and dislike it instantly. Pronunciation I hear was similar to maudelena, so I hope this isn't correct one.
Magdalene would not stand out (that "g" is the only thing that separates it from Madeline, depending on how you pronounce it.) Magdalena would- a little bit. And Maggie in a sea of Maddies? It's really not that different.
The thing about fitting in/standing out names is that they still fit in- which is something parents generally like about those names. It really isn't at all a bad thing. I don't think she'd often be mistaken for Madeleine (that's more true for Magdalena than Magdalene) but it does sound similar. Again, that's not a bad thing. She likely won't share her name with other girls in her class, but the sounds will be familiar enough that no one thinks her name is weird. I love Magdalena and I'd love to meet one!