Custom camera settings allow me to select, for example, a red filter (as I only work in B&W this is an advantage), is there any advantage to using this digital in-camera filter over a real red lens filter when it comes to final B&W image quality?
In general not really. The are potentially some benefits e.g. a blue filter might prevent you from blowing the red channel and getting flare or other problems with excessive light (e.g. sensor bloom) if for some reason you have far more red light.
But generally using a coloured filter will just prevent you from changing your mind later compared to using the in-camera filter (and shooting raw) which to me is a massive disadvantage.
I prefer to shoot color in raw, then do the conversion in post. There are quite a few good b+w conversion tools out there that can do a better job than the in camera filters.
Also, at least with Canon, when you shoot raw the in camera filters can be applied using the software provided with camera (Digital Photo Professional).
To my best knowledge, using strong color filters (like 25A, 38A, 99) on digital cameras have only downsides:
Considering there is no way to avoid Bayer interpolation and all the possibilities that open when doing the BW conversion in post, I'd suggest not to use these filters on digital cameras. So shoot RAW and add the effects you want afterwards.
Here are some examples. Both images were shot RAW, developed using Monochrome Picture Style in DPP with exactly the same settings, shot with red filter had its brightness adjusted and software red filter was applied to shot without physical red filter.
Software red filter:
Physical red filter:
Histograms before monochrome conversion:
And here are some 100% details (physical filter on the left, software on the right):
I'm a bit confused about the sharpening-like effects of the physical red filter version and have triple cheked my settings, sharpening was 0 for both. Lower image is meant to illustrate the differences in local contrast.
Some more details and situations where some color correction filters are usable is provided in this answer: http://photo.stackexchange.com/questions/586/are-colour-filters-worth-using-with-digital-cameras/619#619