(Note, I could be wrong as I don’t know for sure, I just think it works this way. )
If you are talking about this for example:
I would say yes, the filter option applies at all times, because, the option is still available when the Sample Rate Conversion is turned off. So, I would expect it to be applicable to Conversion based on Device Settings as well. It would be weird for it not to, imho.
Conversion based on Device Settings take precedence over DSP Conversion settings, and, happen whether you have DSP turned off or on. If you set your DAC which can do 192k, to a Max of 48k in the Device Settings, if you then go to the DSP section you will find that it is limited to 48k (if you choose custom) as a Max conversion. Even with DSP Conversion turned off, any 192k original source would be downsampled to 48k (Based on the Device Setting, and, again I assume, have the applicable selected filter applied.
But, if we want to know for sure we can always, ask, @dylan.