Can an aluminium frame rust from the inside if water has been in it for some time?
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.