To start off, the QM already mentioned knowing the game due to previous comments given in the thread. I will get back to that later, but this at least means she is aware of it.
First of all, let us look at the mechanics:
In the beginning, we are given one choice for a wish; no limits, just say whatever we want.
This is obviously the same as waking up in the Ruins and being taught the basics by Toriel; this is where it was decided which route to follow.
Upon death, we can return to a previous point in time and try again from there; Determination at its best, even though the QM masks it behind other reasons.
Each arc stars a particular character, all of them antagonistic in the beginning for one reason or another; as per Word of God, all of them can be befriended and I can name you exactly one game that has the very same promise to it.
Of course some parts do not correlate, but this is due to transitioning errors; fighting Witches is mandatory to a PMMM-setting, so nothing can be done about it (even though I suspect from previous comments on the matter that hugging them might lead to unexpected positive results, but that has yet to happen to base my suspicions). However, it works well in disguising what this is actually about, the social aspect.
Anyway, I can gauge three routes here:
First of all would be the normal route, given by most of the wishes chosen. Specifics would change based on what was taken, but going this way would basically always result in the same experience with slight changes. With Tamiko being ignored by most of the world, this is to be expected.
Someone theorised how she might have become bitter and furious with Kimiko upon wishing to find out about who did this to her or why this happened; wishes of that kind could have led to something like the Genocide route, if less extreme.
And then, of course, the path we are on.
By luck/intuition/fate/whatever, a wish was chosen that counteracts Tamiko's main problem and made her... well, run around and basically, in Undyne's words, "hug random strangers"; they are semi-random, but it does still count (especially for prude Japan). That she makes them all her friends does not retroactively disprove the previous statement, either. She hugged Kishi almost right off the bat, after they knew each other for maybe fifteen minutes.
The first actual encounter with Ariane's ghost saw Tamiko hurt, yet she did not let this dissuade her from helping and making friends. The same counts even more with Mariko, considering the pain-reflection.
No matter how often Tamiko is hurt, she refuses to give up on others and holds her hand out to them. This is, without doubt, equivalent to the True Pacifist route.
Now for the characters. It was very helpful for my analysis that our QM already compared aunt Hicchan to Sans; she is goofy and aloof, happy to help out and has a great many tricks up her sleave. On top of that, I can feel that any Magical Girl who ever tries to hurt Tamiko on purpose... will have a bad time.
So we have Sans already referenced.
Looking at it, Ariane's boundless cheer and enthusiasm does remind me of the Monster Kid, both of them very hard to bring down. Tamiko herself makes for a very believable Frisk (... now we have to see whether Kimiko might fit Chara) and Mariko appears somewhat like Napstablook in her behaviour, if a little less obvious.
Kishi gives off some vibes of Alphys, especially with how she tries to carry her burdens by herself; the sciency shtick only underlines the similarities there.
I am not yet sure whether I should file Cathy as Undyne or Papyrus... but it is most definitely one of those two. We have seen too little about her to determine it yet. This goes doubly for Matsuko and Yuujin, considering those two had exactly one appearance so far. Ami, I am afraid to say, is too normal to fit any Undertale-character properly. However, this might only be a feint to dismiss the comparison as a whole with.
Now for Evelyn, who might turn out a reference to some major character in case she contracts; right now however... I have nothing for her. She might turn out to be the actual Undyne, though. It was already stated that MG!Eve uses a polearm, so that theory might have some merit.
Anyway; to conclude, even if there are some things not fitting the overall assumption, those are trivial in comparison to all the similarities there. Puella Magi Memento Mori is, by and large, an Undertale reference.
Q.E.D.
You can admit to it now,
@DrZiztah.