http://dissertations.jyu.fi/studcomp/951391707X.pdf. There everything about RR-I, HRV analysis and EPOC calculation is explained in very detailed.
To answer one question: “Is there actually a variable in the EPOC accumulation equation for HRV which causes EPOC to accumulate differently (faster slower at same intensity one day vs. next) based on the fatigue levels in the body?”
In simple, the rate of EPOC accumulation is calculated by comparing the changes of the intensity level (%VO2max) in consequent time points. More the intensity changes, more rapidly EPOC accumulates. HRV analysis comes to the question, when estimating the intensity level (using RespR and on- and off-dynamics of the VO2).