Some differences I noticed:
Just opened both URLs side by side (in Chrome on Mac) to check your findings.
Regarding music: Yes, that's right. armanelgtron has converted the MODs to OGG music files, while I did not change anything (so you can see three warnings in the browser console about not being able to load those MOD files).
Maybe I'll use his converted music files when "officially" announcing the R'n'D browser port. (As I intend to only use it as a preview for the "real" game, I think it is not that important. But then, it really plays quite well in the browser, so also having music would be nice, of course.)
Regarding display size, I can see no difference at all -- it's exactly the same size for me (pixel-exact original size, unless you change the scaling in the setup menu).
Regarding browser keyboard commands, I was also unable to notice any difference. (Tested with some standard keyboard shortcuts, like opening a new browser tab etc., as there is no Ctrl-1 in my Chrome.)
The favicon could be explicitly added in the "index.html" file of the browser port (to use a different one), but here it simply uses that of the main web site.
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More interesting, in my opinion, would be the following three potential enhancements:
1. Store local changes locally in the browsers internal database (using Emscripten's IDBFS). This would make ist possible to store setup changes, newly created levels, tapes and scores between browser sessions, which would be really cool.
I think it is not too difficult to add this, and I will at least have a look at this sooner or later.
2. Load remote files from the web server. This would make it possible to dynamically access files like levels (also from new levels sets added later) and configuration defaults for the browser port (which currently either have to be hardcoded into the game, like the different rendering mode used for the Emscripten port, or would require packaging the game with an adjusted default configuration file, just like the "Mirror Magic" or "R'n'D jue II" packages do it).
I am currently not sure if this would be easy to add or not.
3. Store files to the server. This would be nice for centrally storing high scores and solution tapes, and would also need adjustments in handling these assets in the game.
This would probably require more work than the two above tasks.