Nope, it's just as easy if not easier to mod the Steam version now.
The Steam version puts the file updater on your computer that comes from Ubisoft. That file updater/loader installs the latest update (v1.2).
Moding is done the same.
The beauty part of Steam is no boxes or discs to keep track of and if you do munch your install, a "verify files" will fix the install back to stock. You just have to re-apply your mods.
The actual process would be
Un-install mods
Verify files
Re-install mods
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