Yocto's a pretty huge system, understanding the nuances is quite hard. I believe you're probably confusing patches and recipes.

To me, it looks like everything works as intended:

• BBFILE_PRIORITY_meta-mylayer controls the priority of recipes
• A .bb or .bbappend (aka recipe) overwrites the variables previously set by the same recipe in other layers.
• Thus, higher priority will result in is parsed later
• To bitbake, your patch is nothing more than a string in SRC_URI for that recipe. It behaves as I described above.

If you want to change the patches that are applied you can remove patches from SRC_URI in your recipe.bb file:

SRC_URI:remove = "foo.patch"

Similar to how it's done for local.conf: Yocto: Is there a way to remove items of SRC_URI in local.conf?