Far fewer than who offer the service, though if you ask a question about it here every single one will be recommended by someone...
It's not like the mfg don't know what they are doing (though they mess up occasionally), so most of the time it's more about perhaps tailoring the power band.
One thing that the mfg need to consider is that the engines might end up in different locations, different altitud over the sea, different fuels, different tuning skills etc etc, so things like head shims can be a little bit on the safe side (sometimes).
If you look at the offroad side, probably 90% is running a small carb insert, and they still send in engines to get modified, talk about placebo effect from visual appearance...

Totally agree.