Hope you are doing well. Sorry for your experience with using the combine files tool on Acrobat.
The combine tool usually just merges the files as they are, without any modifications.
What you can do here is click the three dots to the top right > print > change the page size as per your requirement > click the share icon to the top right> and click "Save to files."
Once done, you will see a new file being created with all the pages aligned to the same size as you selected initially.