It seems that ryujinx can't handle multiple @enabled @stop blocks in one file, only the first section is used, and the rest are skipped. This can be seen by running the 60fps mod on a slow computer, the game runs in slow motion because the lower dynamic portion isn't applied. Combining the fps and dynamic portions into a single block works as intended.
This also means the visualfixes mod currently does nothing on ryujinx, since the very first block is @disabled, and the rest of the blocks are ignored.
It does appear that a comment line in the middle of a block works as intended, so if you'd like to improve ryujinx compatibility, you will either need to separate the patches into individual files, or combine them into a single @enable @stop block, and use comments to separate the sections. Commenting out the disabled patches will probably works as well. I'm unsure if commenting in the middle of a block will affect yuzu, but if not, this method would work for both emulators.
In addition, once the mod is fixed, it seems that the LOD section of visualfixes causes an instant crash upon loading the game on ryujinx.