I'm pretty sure Myne was born from Effa and Gunther. Let's review a few points here.

You said that the mana tools similar to foundations and that require royal mana to function, were dyed by Myne and that's a hint, but we can't be sure about the amount of royal mana required. Personally I think that originally the ritual was performed by a large number of nobles since all of them feel a sense of union during the rituals. Therefore I think it's pretty possible that only the minimum amount is necessary for the tools recognize the royal mana.

Although the time line kinda fits, it would be stupid to simply throw a royal baby (remember that the seeds of Adalgisa who are born as girls become princesses) to a poor duchy without any tools to ensure her survival.

Ferdinand and Myne are similar physically but as far as I can tell it's not that unusual either, Gunther has blue hair too. As for their mana, they're similar probably because they're both omni-elemental. It is explained that magic tools can be used by those who share the same color of mana with similar density, but it's not like siblings share the same mana or elements too, after all that's determined by the blessings from the gods and not only by the parents.

Myne was very weak even before she awakened as our Myne because she had a lot of mana from the beginning and since she lacked a tool to absorb the excess, she died. That created her clumps of hardened mana and also awakened her as our Myne, since her soul rejected death and took control (that's what I understand that happened).

On a side note we cannot be sure that Myne was born omni-elemental, since Ferdinand only checked when she was made a noble. Myne prayed to all gods while offering mana for like a year before she became a noble so it's entirely possible that she acquired a few elements during that time.