Yes the nam file needs it in the metadata for this to work. If it’s not there it doesn’t offset any levels. It would probably just use the hardware level whatever that is (+8dBu, +12dBu etc). If you open a .nam file in a text editor you'll see a lot of metadata in there, here's one of mine trained on Tone3000 where I told it to use +13dBu
"name":"EVH-5153-Blue-G5","modeled_by":"ampspedalspickups","gear_type":"amp","gear_make":"tz-make","gear_model":"tz-model","tone_type":"overdrive","input_level_dbu":13,"output_level_dbu":null
If your hardware is set to say +12dBu and the NAM file is set to +15dBu then your hardware is hotter than the profile needs. You'd back the input level by 3db to compensate. If your hardware was +13dBu (my RME) and a profile was +8dBu then I'd need to gain up the level by 5db to match.
I'm not sure what level the stomp station is on the hardware but it would just be offsetting those numbers where it can read the metadata. If there's no metadata to read it will just use whatever the hardware is and then its up to the user to "use your ears bro".