Many operations in Photoshop only work correctly in RGB mode, they may not work in Lab or CMYK modes as they do in RGB mode.
Something does not sound right, however…
If I am understanding the situation correctly, you have issues with the “standard RGB ICC workflow” converting from a wider gamut source profile direct to the inkjet destination profile (CMYK profile that is wider gamut than standard press CMYK). You are using a perceptual transform from the wider gamut RGB to an intermediate press CMYK working space for final edits, before going to the inkjet device CMYK.
Why not just perform all edits in RGB, then convert to the F39 press CMYK profile, then to the final device profile if this is what works for you. It is not so much the edits in press CMYK space, but the conversion through press CMYK to the final profile that works for you.
As an alternative to using a standard offset press CMYK as an intermediate space, you could try using the following “PhotoGamut RGB” profile to convert from wide gamut RGB to this profile, then to your final device profile. This RGB profile has a wider gamut than standard offset press conditions, if also offers a perceptual transform from the source into PhotoGamut RGB and it is “well behaved” so R=G=B which will allow you to use high pass, desaturate etc.
Info: http://www.photogamut.org/E_idea.html
Profile: http://www.photogamut.org/E_ICC_profile.html
Here is the PhotoGamut RGB colour space (ghosted) compared to Fogra39/ISO Coated v2 (colour):
