To address the artificial gravity, I believe it is caused by raising the effective mass of the ship to the point that it projects gravity to the degree of a planet the size of Earth. As I understand it, mass is the determining factor in the force of gravity an object projects. All objects have gravity, but the strongest gravity overrides the others in most circumstances. The space magic comes in when you go at FTL speeds (requiring a nullifying of your mass) and still running artificial gravity (requiring a huge raising of your mass) at the same time.
There are many aspects of Mass Effect that are poorly explained. Most of the time, they have the decency to at least kinda have it make sense, unlike Star Trek, for example, which uses technobabble for almost everything. We as fans have gotten a little too used to this, and so when the writers use artistic license a bit to get their point across, we cry foul. It's perfectly understandable, but we need a bit of self-awareness about this.
The Thorian and the Cipher are space magic. The Rachni and their ability to take control of dead bodies is space magic, as is their genetic memory thing. The Prothean beacons and their ability to sense who you are through touch is space magic. Asari reproduction is largely space magic based. The way indoctrination works is space magic as well, since we have only observed the effects, we still have no clue how it actually works. And so on.
People draw the line at synthesis largely because it is introduced suddenly and is massive in scale. That seems to be the main problem with it. And I say all this as someone who supports synthesis, for the most part.