Perspective can change. But the fundamental lore should not. "Understanding is a three edged sword. Your side, my side, and the truth."
Take Solas's description of Loghain's act at Ostagar. Was he a valiant general trying to save as many lives as he could when a situation became untenable? Or was he a traitor who abandoned his king to die? Based on details known and points of view taken, he could be either. But it does not change the facts of what he did. He pulled his army out of Ostagar. King Cailan died. These are undeniable truths.
There needs to be set facts within the setting that are off-limits to change, even by the writers. If we the players have details deliberately hidden from us so something can be sprung upon us later (like the rachni egg) then fine. Plot twist! But changing the foundations of the setting because you painted yourself into a corner is...not so good.
"Expand upon what you already have before you add something new" Sanderson's Third Law
Besides which, discovering a means to travel between galaxies in a Mass Effect setting is big enough it could warrant a story all on its own. But then, someting like the Lazarus Project would too...
I can't think of a single instance where the foundations of the setting have changed though, outside of what is described like the rachni queen or the thermal clips, which are again made for story-gameplay reasons.
That is what it boils down to. Perspective of events is always fine, but changing how things work, or giving perspective that contradicts understand of events or how things work, should also be fine at the same time. The Lazarus project makes no sense scientifically, but it was done and used as a plot device, and as a metaphor, for Shepard story-wise, and as a gameplay mechanic for the game.
If, for example, they upgrade FTL travel and give you in-ship mass effect fields or technology or something, without using Mass relays, the simple solution they have to say is technology has advanced for it, or they reversed engineered technology, or they finally harnessed Mass effect fields into smaller chunks, whatever the case may be. We get a codex on it that explains the discovery, and boom, instant plot point or justification for a gameplay mechanic.
Is that really lore-breaking in that sense? To me, that is the same as resurrecting the Rachni; it is changing the established descriptions.