Something unsaid with the thread is Liz has to have a plan to save Makoto If she came back in time. At no point have we asked what it is and we're running out of time.
Because Liz is Liz. So what terribly unwise thing has she thought up.
The assumption I've largely been operating under, based on the general vibe I got, is that she doesn't intend on actually interfering with Makoto's Journey or the outcome of that Journey, but is more here as part of the long game. She feels more to me like she's taking this opportunity to learn by observation + surface interaction, and get her own Journey off to a slow start; she's deliberately hung at the back, mostly left SEES to handle everything they did in the previous timeline, and in general, becoming the Great Seal instead of Makoto feels more like it'd be a desperation play from Elizabeth at best rather than a legitimate plan.
However, she might well be in that position of desperation--or I could be misreading her. A serious blindspot on my part was that the only idea I had really considered for how she might attempt to interfere with the outcome of Makoto's Journey was in becoming the Great Seal, and even if we take as a given that she won't do that, that doesn't preclude her having other ideas, as you mentioned. And again, as you mentioned, those ideas...could very easily be of the extremely inadvisable sort.
And with the conversation we just had, this is probably one of the more likely chances we'll get to go to her and potentially get some sort of answer that relates to this subject.
...Only tangentially related, something I've been thinking about: the option we selected after the botched rescue, to talk to Elizabeth, had a hidden (+Empathy) to it. The person who died wasn't mentioned in the following conversation, but considering that interlude, I think one of three things happened:
1) The death itself affected her enough for it to count toward Empathy
2) Her Social Link with the one who's still alive either reversed or broke, and
that affected her enough for it to count (this doesn't seem that unlikely to me, with how that interlude ended)
3) The Social Link either reversed or broke, and both events affected her enough for it to count
I don't imagine we'll find out for a while regardless, but I thought it was worth mentioning.