Again, the biggest problem is typically not the transmission itself, it's the clutch. Yes, a very low first gear ratio can be selected to make it easier on the clutch, and in a 13-speed heavy truck transmission that's fine, but in a light vehicle 5-speed that's an undesirable compromise. A high-capacity clutch could be used, but people don't want a heavy and long-travel clutch pedal. And then there's generally incompetent non-commercial driver which the vehicle manufacturer can't control (unlike the automatic transmission that they can), which may be the biggest factor.
The net result is that in a vehicle like a Cherokee, the towing rating will be lower with the manual transmission, regardless of what could be done with a different vehicle under different circumstances. In full-size pickup trucks, when they were still available with manual transmissions, even the manuals had high towing capacity... but almost no one wants to drive those things. The Cherokee is sturdier than a Freelander, but still basically just a car; it's not a commercial vehicle. Some Cherokees have the same transmission as some pickup trucks, so for some of them this isn't the vehicle's towing limitation.
The details don't matter to an EV conversion anyway, except that if a manual transmission is used the lower towing rating rated to the clutch can be ignored - the electric powertrain will become its own limitation, and no one will determine that for the builder. The strongest manual found in a XJ Cherokee is probably the New Venture Gear 3500, but even though it was used in full-sized pickup trucks it would be marginal for the load considered in this conversion... regardless of the clutch.