There are some practical downsides for the purpose of current backwards compatibility in trem (in particular related to supporting the 1.1 vanilla stock client from trem.net which unfortunately many people still use). The 1.1 stock client can only download directly from the game server, although thanks to an improvement to the game server by @DevHC, the newest multiprotocol trem servers can offer download usually around 100kb/s and beats the old 3 kb/s (which even gpp had, but everyone used the web downloads, so it was hardly ever noticed).
The other issue is an old bug in the game servers that hasn’t been fixed yet where the downloads of pk3 files over 32 MB freezes at 32 MB. Again, with the web downloads, this bug was never really a noticable issue for clients and server that used web downloads, but for the 1.1 vanilla stock clients, and servers that want to still support them it is.
These are just some factoids to consider, there are many maps that include .map files that are still manageable for backwards compatibility. In the case of this version of pulse, the size of the most recent pk3 file without a .map is 21.7 MB, the size of the .map (uncompressed) is 8.4 MB, so the resulting pk3 would be X amount less than 30.1 MB, which is still under 32 MB, so it would still work.
More players are upgrading to the 1.3 alpha client ( found here: https://github.com/GrangerHub/tremulous/releases ), and many of them were using the 1.1 vanilla stock client right before, so hopefully at some point enough people will be upgrading where the above mentioned issues will become moot. But yes, keeping the .map in the map pk3 is definitely good practice in general.