Indeed that is the question, but I don't think the answer lies in trying to add a parameter for every mechanistic variable (eg: gradual changes in electrolyte balance) which makes for an ever increasing level of complexity model. Fatigue and performance are essentially two sides of the same coin, and these are outcome variables, not explanatory variables. This is what W'bal is trying to acheive though, not necessarily explain the precise mechanism. For example, I don't think it is necessary (for the purposes of work-balance modeling) to attempt to model glycogen depletion, because it isn't the only thing that leads to long duration fatigue. Just try to model the fatigue/performance itself under some "standard" or optimal condition (which would need to be defined... eg: temp, humidity, CHO and fluid intake). Deviation from the model could be the result of many variables. So rather than try to model ALL of the possible variables that could affect performance (which is unknowable anyway) so that your model stays perfectly accurate all the time, you just understand that something (without knowing exactly what) is causing deviation.
Something that I\ve found when comparing the differential W'bal model to the integral model (using LMM stats) is that there are minimal deviations between models for computed W'bal when minimal fatigue exists (eg: W'bal stays above 60-70%), but when W'bal starts dropping and exercise bout, either constant load or interval, approaches a maximal effort, then the model's differ significantly. Anyone using W'bal modeling at the moment in GC would note this already. So my gut feeling is that we might expect something similar when we compute W'bal with an "optimised" model that takes into account slow fatigue. ie: if something causes deviation from the model like illness, it won't be very apparent in the low fatigue W'bal zone of 75-100% unless you also tag your RPE thoughout a session at very submaximal levels. Where the extraneous effect will become very obvious though is whenever a maximal effort is being produced. Then you know for sure, your lack of CHO, sleep, recovery from previous training, illness, the ambient temp (its hot today) or whatever, is making a serious impact on your ability to drop W'bal to zero later on in some highly random workout.