EMT "Legacy Mode" is an option that's available to run when "Virtual FSX" is enabled. It can be run from the options listed under Flightsim Estonia on the startup menu or from the P3D v1/v2 root folder.
EMT "installs" a temp fsx.exe file and sets up links to other folders which aids in installing FSX addons into P3D. The fsx.exe file that's placed in the P3D root folder is "active", in that, when run, creates and places a hard fsx.cfg file entry in the Lockheed Martin Appsdata folder that mirrors the prepar3d.cfg file. It's a little more complicated than that, but that's the "jist" of it.
The only addon program I use that required "Legacy Mode" to run properly in Prepar3D v1 was EZCA. EZCA "looks" for the FSX process entry in the registry and then for the fsx.exe file in the root folder. EMT "Legacy Mode" temporarily substitutes these entries without making any actual hard changes in the registry or root folder. The ONLY time the fsx.exe file can be active is when expressly running "Legacy Mode" after enabling "Virtual FSX" in EMT.
There may be other addons that require this, but I don't have them.
Prepar3D v2 has eliminated, for me, the need to run "Legacy Mode" when using EZCA. The only time I run EMT now is configure EZCA active camera "201" entry into newly installed addon aircraft.
Many vendors have added dedicated installers for Prepar3D v1 and more are working on the same for v2. Due the serious health issues Marniftarr is facing, there will probably be no EZCA v2 which was to be designed to work directly with Prepar3D as well as FSX.
Hope this helps.
plug_nickel