If all files' names match it doesn't matter, but generally it isn't a good idea: If the old version had a file that is not included/has a different name in the new version if will not be overwritten and that can cause weird issues.

The 1.6.6. installers have been released and now the Linux version contains even more copies of the game's data. It's a whopping 3.3 GB compared to the original 446 MB.

I still have to even install the game (was very interested in it when I bought it, but I just can't find the time for it), and was wondering about the installer sizes. The installers for Windows are: 1.6.4 = 449 MB, 1.6.5 = 853 MB, 1.6.6 = 1.08 GB ... <facepalm>

Yeah, cause its include older game versions too.

When you start a new game and check the box for "show all versions" you are able to chose between 1.6.1 1.6.4 1.6.5 or 1.6.6.
You can see the correspondig files in <Tales_install_dir>/game/t-engine4-linux64/game/modules/
And here is one more copy of this all for the 32bit Version:
<Tales_install_dir>/game/t-engine4-linux32/game/modules/

So you obtain max compability (32 and 64 bit, you can use older game versions for older save files), but have a bloated installer and a big game directory (4,5 GB).