To elaborate a bit more, I've seen 3 types of mods types (for installs)
1 - Overwrites / swaps existing files :
This is a straight up take files A-Z and copy paste them over A-Z in the original file locations. (Always make a backup of the original files/folders first.)
2 - Placement in the BATTLETECH/BattleTech_Data/StreamingAssets/mods/ folder, with VersionManifest.csv and/or MetadataDataBase.db edits :
In this case, the mod is placed in a newly created mods sub-folder in the BATTLETECH/BattleTech_Data/StreamingAssets folder. Then lines are added / changed in the VersionManifest.csv file (in the StreamAssets/data folder) to allow the game to see these new files (or to point to these files as the default, instead of the original ones). In order to get things to appear in the campaign, the MetadataDatabase.db file (in StreamAssets/MDD folder) usually needs to be edited as well.
3 - Placement in the BATTLETECH/Mods folder (notice the capital M) :
In this case, you are placing the mod in a folder for the BTML/ModTek to properly find it. Mods made to work with BTML/ModTek have a mod.json file in their root folder. This file provides BTML/ModTek with the 'roadmap' of what folders in the mod correlate to the base game folders, and then load them into the game. Additionally, the mod.json file has a line in it that toggles if the mod is Active or not - which is a simple true/false trigger.
To answer your question further - yes, you could place mods in the BATTLETECH/Mods folder prior to installing the BTML & ModTek, but they are not going to do anything until BTML & ModTek are installed as well, as the game otherwise has no way of knowing it is there.
Hope that helps!