The thing is...usually only raid exclusive pokemon have its shiny chance increased (Mawile, Absol and Shinx). The rest have the same chance as a wild encounter so i wouldn't spend my passes on magnemite raids. Regarding your question the level is the same when you catch the alolan eggy be it from a lvl 2 or 4 raid, only the rewards change.
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Alolan Eggy raid boss
For a reasonably long time, Alolan Eggy was an on again off again tier 2 raid boss. I took advantage of the opportunity to take down a lot of them, and got a few good ones. Now it's back, but as a tier 4. Aside from the extra candy and loot, is there any other advantage to taking it down as a tier 4? And is this the beginning of a trend? Magneton was a tier 2, now Magnemite is a tier 1. Would rather find them wild, and save the pass for better bosses. Of course, a weather buffed shiny would be the bomb, ....
