Hot answers tagged rain
While the aluminum frame itself will be relatively ok, the problem will be your bottom bracket (almost certainly made in part of steel) which was most probably sitting in a big puddle of water. Even if the water didn't cause the bearings to rust, a freezing/melting cycle can cause damage to the bearings themselves, force lubricants out, and otherwise mess-up ...
Technically rust is limited to iron. What is bad is the rust starts and continues. The water / oxidizing agent is not consumed. Aluminum will oxidize but it forms a protective coating. An aluminum frame will not "oxidize out". Some iron alloys such as stainless steel prevent rust. I don't know why you don't seem to see stainless in bicycles.
Is the frame pure aluminium? Aluminium does not rust. If the frame is an alloy you would need to check whether or not the other materials are susceptible to rust.
If its better integration of rack & fender you seek, look into getting a rack with a centerline stud or nut that you can attach the outmost half of the fender to. See this pic for a rear fender+rack example.
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