When installing SMAPI normally, you have to type the filepath of StardewModdingAPI.exe in Steam launch properties; in my case, this is:
"C:\Gaming\Steam\steamapps\common\Stardew Valley\StardewModdingAPI.exe" %command%.
If SMAPI is installed via the new Nexus Mod App while the above launch options are set, Steam returns a "missing game executable" error. It seems that SMAPI is only placed in the game folder when the game is launched via the Nexus Mods App.
So do Steam achievements still work, or do I have to take additional steps?