to me the question is more about user experience than results--at least it seems so from how you framed the issue. both systems are going to yield very good results, which you realize already. both have film like color qualities and both imo lead the league in b&w. both are excellent with skin tones. so really on pure IQ in good conditions for your purposes its a wash.
the obvious difference is af vs mf and no one can help there.
the next 'obvious' difference is high iso, depending on which fuji you get, 6400 is very useable vs 1600 which is very useable on the rd1. i personally found fuji overrates their iso, so to my unscientific feel, 6400 on fuji would equal 3200 on the rd1 if such a thing were possible. IOW, its about a one stop difference between fujis and epsons iso ratings.
my fairly inexpensive solution for some time has been to have the now cheap original x100 as an af/high iso complement to my rd1. if thats not for you, again, i think the essential issue is your personal evaluation of the user experience. if as i do you get really jazzed by using the rd1's ovf and rf focusing then dont overthink it and just get the rd1; if not then you should go for fuji.