When you extract file and create a new folder/directory, then off course it is treated as recently modified, because you just created it. This is much different than just extracting a directory from archive as it is to preserve its original attributes.
I just tested and observed following:
Open archive file by double clicking in the default application Ark (with GUI). Extract a sub directory from the archive by dragging it out into my filemanager Dolphin. The original last modified date is preserved.
On the contrary, I right mouse click the archive in my filemanager Dolphin and use the Extract > Extract here menu entry. This will extract the files and the sub directories have new last modified dates, but not the files. This does not need any manual folder creation by you.
I assume you want to solve this by only using the GUI. Because using commandline in the terminal these stuff could be solved. With a script this can be even automated. On the other hand, maybe you (or someone else) could create a script with the exact behavior you wish and then you can just right mouse click on the archive, and choose “open with … the_special_script”, which also updates the folder with newest last modified date in example.