About the giantess from the beggining, I really have zero clue on who it could be, maybe someone from Homaspernia but that's just an assumption, but I am sure it is none of the characters that appeared so far.
About the mc's amnesia, it is very weird that whatever happened to him, there is no trace of magic. None of the things that are particular from that world (like giant plants, animals or structures, magic and giantesses) seem to ring a bell in his head, but he knows what the common things are.
It makes me think that a giantess opened a portal to "our" dimension (where there is no magic and we are all purebred) and kidnapped him from there.
The last problem is his first memory or "dream", where he was in a cage. How did he got to a neutral town? Or a better question: why his kidnapper allowed him to escape or left him there?
I think that the one in the prologue is some sort of celestial creature that collect souls and put them in the real world for fun or something.
I don't think that MC has amnesia. Amnesia is a condition, under which a person
forgets things, while MC literally has no past, like he never existed. At least, that's what everyone says who ever checked his memory, even Cygnia. It raises some questions about his basic abilities though, like speaking, walking, etc.
I'm not sure if the story is really an isekai, lol. The fact that he is both purebred and puresoul doesn't necessarily mean that he's from another universe, it's just a rare occasion. But since there are 0 clues about MC's past, the odds that I'm wrong is as same as that you are I guess.
From dialogues with Orphileth we know that he was brought there and taken care by unknown people, which raises even more questions than giving any answers, yet it's a hint that he might've used live there and actually lost memories about a life he once had.