Joining two pdfs with slightly different page size with pdfjoin
Solution 1:
pdfjoin --paper a4paper --rotateoversize false
does the trick for me. rotateoversize is the important option
Solution 2:
pdfjam --paper a4paper file1.pdf file2.pdf did the trick for me using one letter-sized document and one slightly-not-A4-document, they're both joined as A4 as expected.