Mary Magdalene isn't consistently named in the NT. In Luke 8 it's 'Mary called Magdalene' (ie Magdalene is an Aramaic nickname) that's not the same as 'Mary Magdalene'
The chances are there are various Mary's in the gospels - but more than likely some of them are identical to the one named Magdalene.
I see no reason why they should be a consistency rule for her mentions, how consistent are the disciples names when they are named? (i can't answer that right now, but i'm not sure it's always consistent?)
Anyway, as for a companion her role in John kind of implies that far more than Thomas does! I never thought of her question in logian 21 being her separating herself out as not a disciple. That's actually quite interesting. I suppose it might, but only if you read it that way
So what you're saying is a late role of companion is baked into John's gospel already - which is 'late' only as John may be later than the synoptics
So your argument only pushes that date of Thomas to around the time of John's gospel that's not very late. I think a revision of Thomas around that time is possible, but other than that I agree with ML Thomas is a source to the gospels
Mary is rebuked in the NT at the anointing scene. That this is Magdalene is really a case of 1 + 1 being 2. If she is very close to Jesus given the information already in John's gospel, the Mary who anoints him at this key moment is the same one who is there in the other key moment
Mary, therefore, took a pound of ointment of pure nard, very precious, and anointed the feet of Jesus, and wiped his feet with her hair. The house was filled with the fragrance of the ointment. 12:4Then Judas Iscariot, Simon's son, one of his disciples, who would betray him, said, 12:5"Why wasn't this ointment sold for three hundred denarii, and given to the poor?" 12:6Now he said this, not because he cared for the poor, but because he was a thief, and having the money box, used to steal what was put into it. 12:7But Jesus said, "Leave her alone. She has kept this for the day of my burial. 12:8For you always have the poor with you, but you don't always have me."