In many cases, a hybrid system uses a planetary set with multiple power inputs (IC engine and [electric] motor). The power sources work individually on say the ring and the planetary carrier, while the sun gear is used for power take-off to the wheels. (I might have the arrangement assigned wrong, but the principle is basically the same. It's a beautiful ménage à trois accomplished with brilliant angineering.) There's the "magic" you spoke of.
This arrangement allows for a multitude of strategies, including all IC, all electric, IC engine starting, regenerative brakes, and various combinations of recharging and motive power. The so-called "Hybrid Synergy Drive" is largely a Toyota effort, but is also licensed to Nissan and I beleive was co-developed with Volvo. Ford and their associated buddies use an Atkinson-cycle engine with variable strokes. This engine is highly efficient in a very narrow RPM range, and has a very narrow torque band. BOTH of these systems use a form of transmission that could roughly be called "CVT", with a nearly infinite number of gear ratios to optimise efficiency.
For one of the reasons you mentioned (broad torque range of [electric] motors) a manual transmission in this system is not only not needed, but would probably be in constant conflict with the various power/regeneration distribution models - which are delicate formulas constantly changing and adjusting for efficiency. Something only a computer can do well instantly, continuously, and with an inherent understanding of of the horsefeathers and unicorn blood that makes these things work. You might be able to make an educated guess on gear selection and execute a choice, but probably not a thousand times a second.
(Whilst there should be no need to put [electric] in front of "motor", I do so for clarity... and the admission I'm one of "those" people...)
On a vehicle with drive [electric] motors at the wheels (e.g. Tesla) there probably is no need for any selectable gearing at all. On a "hybrid drive" scenario with both IC and a single [electric] motor as power sources, the computer must control this operation and torque splitting. It is doubtful that a 5,6,7 speed manual system (perhaps with a clutch?) would work in the ideal efficient fashion these vehicles are intended to perform.
Contrast the "performance" aspect of a niche vehicle like a Tesla, vs. the "eco" effciency of a vehicle like the Prius. Neither (in particular) offer a true "manual" transmission, and I would suggest that neither needs or would benefit from one. High performance "sport" vehicles (including Tesla, to some extent) usually cannot feature a highly efficient CVT transmissions, as these transmissions tend to be limited in torque handling capability. Perhaps in years to come.
And as a final divergence from a different perspective, only gearhead weirdos such as meself refuse to trust juice boxes. Largey due to my age and thickheadantry, but my point remains. Who would buy it? You can't even sell a modern V8 muscle car with sufficent market penetration in a "stick only" scenario. Those days are long gone. [sniff] You might see 10-20% stick sales on a very top-end Corvette, Camaro, or Challenger SRT. So, besides the practical engineering/efficiency aspects, I doubt any serious hybrid/electric OEM would even consider a manual transmission vehicle with such a poor ROI given the development costs. Build it and they will NOT come.