I too had this issue. It seems there may be a few issues with the v2.2 679 build download for Rutile Ruby (for one, I had to manually modify the link to get the right address). Corruption44 had reported above that he had issues with the pokemart and suggested replacing the code.bin. However, I was able to get the proper behavior from the pokemart in the uploaded build and received honey before I fought May. However, I used a similar approach that corruption44 used to fix the encounter tables, as it seems that the code responsible for modifying the grass was not included in the provided v2.2 build. Instead, it just has the Legit Build, or non-modified, encounter tables. You can add in the 679 modified encounter tables by replacing some of the files from a previous version.
1. Obtain a previous version of the CFW "Compile Your Own" installation. OP posted a reddit thread that contains some older DL links here: https://www.reddit.com/r/3dshacks/comments/4m7chs/pokémon_rutile_ruby_and_star_sapphire_20_oras/
2. Extract the zip file and navigate to .../Encounter Type/679 Build/
3. Copy the file "a"
4. Navigate on your SD card to /luma/titles/000400000011c400/romfs
5. paste the previously copied "a" file and overwrite existing files.
And that should do it! I was able to find a Larvitar in Rusturf Tunnel after doing this file modification. I can't guarantee that this is a 100% fix, and I would advise looking out for when OP reposts the 679 build.
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