I find GW bases are around 2.5mm deep on the underside and N42 magnets are strong enough to pull themselves off superglue (not the model off the magnet but more the magnet off the base). So for a flush fit you'll want to put a little bit of greenstuff underneath.
I'd put the glue on the base, then add the greenstuff then press the magnet on top - that way you should get glue holding both sides pretty strongly. I would then press it down onto a flat surface (not the magnetic tray because you want it flush not sticking) and then lift it up and turn it over to dry (so you don't get glue dribbling down and sticking it to the flat surface.
After that for added support you could pack some glue and greenstuff around the magnet as well.
Also when placing the magnet try to put it underneath the point where the model joins the base, so that when you're lifting it up you're lifting at the join area and thus putting the least amount of pressure on the join itself. And now that I type that I'm pausing and thinking wait you want it far away from the join so that when you lift on the join it acts like a fulcrum on the magnet reducing pressure?
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