If you look at the files that are "newer", you will see that they are images and other support files that do not change. In the case of these type of files, the creation date doesn't matter. I've been overwriting these files for a long time without any problems.
It is unfortunate that Adobe refuses to fix Extension Manager and include an "Overwrite all Older" option to give people some peace of mind. It is very tedious to review every single file. Fortunately using the "Overwrite All" works fine for WA extensions.