Right now, plugins installed to the game directory will only load plugin-specific config files with the path /Project/Plugins/PluginPath/Config/*Default*PluginName.ini. However, engine plugins will only load from /Engine/Plugins/PluginPath/Config/*Base*PluginName.ini (as well as Project/Config/DefaultPluginName.ini for game overrides). Both will also load PluginPath/Config/Engine.ini for patching. These rules are confusing, and it means that you cannot copy a plugin from game to engine or vice versa without renaming the config file. This causes a lot of problems with third party plugins like marketplace ones, because those can be installed to either directory depending on what the launcher decides. Related to this and other confusions, most marketplace plugins avoid using config entirely.
There are several possible solutions. One is to keep the Engine plugin path the same but change the Game plugin path to load /Project/Plugins/PluginPath/Config/*Base*PluginName.ini as well as /Project/Plugins/PluginPath/Config/*Default*PluginName.ini. This should do the right thing in all cases, except if there are third party plugins that worked around the old problem and duplicated the file with array + config entries, because those might duplicated. Another fix would be to try and do something more complicated to detect the right ini file.
There does not appear to be a good plugin to test this with, so here are the rough steps until this can be filled in with a concrete example:
There's no existing public thread on this issue, so head over to Questions & Answers just mention UE-121726 in the post.