I hear what you're saying about the algorithmic/linear application of specific cognitive-behavioral worksheets/techniques, but...
In my experience (granted mostly in a VA setting these past years), protocols hardly apply themselves to people with any level of significant psychopathology let alone co-morbidity.
There are engagement/motivational issues to address with most patients...these will be heavily resistant to automation (I suspect). Anyone who has tried to incorporate 'self-directed' learning/therapy with this population (or, likely, any other) involving workbooks, worksheets, algorithms, websites, or phone apps I think has likely had at best 'mixed success' with them.
There are important case formulation tasks that involve integration of a) test data, b) self-report, c) direct observational data, d) years of clinical experience + experience being a human being trying to navigate human life tasks, motivational slumps, tragedies, interpersonal betrayal, etc..., and e) the basic and applied empirical literature---all of which have to be compared, weighed, cross-checked, and synthesized into a coherent treatment plan and then negotiated and explained to patients. Ongoingly. Often in real-time.
Ever since 'Wanted: A Good Cookbook' we've been seeking a 'holy grail' of {input: patient and diagnosis, testing data} ---> {output: optimal treatment plan} but beyond broad strokes and certain modular sub-protocols (e.g., the sleep restriction algorithm in the CBT-i protocols/phone apps), I haven't seen anything too impressive in clinical practice that doesn't need a clinician 'pilot' to bring it in for a successful landing. Even Meehl was outspoken about the need to include in our actuarial models 'inputs' that come straight from the clinician (e.g., how to actually detect bona fide psychotic symptoms [basically a rating or determination from a clinician [clinical judgment]] which is then fed into the algorithm.
Ultimately, it's an empirical question. We should have a decent approximation of an answer in 10-30 years. Meantime, the patients continue to queue up for effective psychotherapy.