I absolutely don't understand this trend or feature of riding jackets to be mesh outside and water resistant / repellent inside.
It's a cost saving method in at least 2 areas, an aesthetic choice in one, and a performance choice to a lesser extent. For what it's worth, this isn't particularly unique to motorcycling gear either.
Cost: You're putting the hard wearing abrasive exterior on the outside, and the softer, more fragile waterproof liner on the inside. The mesh will also catch some of the moisture and drain it away, even if it's not very effective, but this allows you to use a less durable, fewer layers in the waterproofing layer. Additionally, the waterproof lining needs to attach to the jacket somehow, and using internal loops is generally easier to work with as all the stitching is on the inside of the jacket's outer layer. My waterproof and thermal lining uses a zipper and some loops, and attaching a zipper in the same location would mean adding a seam or button to the mesh exterior at the same location. The attachment process is much simpler by putting things on the inside. By far though, the fragility of waterproof lining is the reasoning I would apply here. I haven't had the greatest success getting waterproof and thermal lining replacements from the manufacturer.
Aesthetics: If you put the lining on the inside, you can make it almost any color, appearance, etc. you want while maintaining the aesthetic looks of the outside. Considering that moto manufacturers don't even really bother to produce large variety in colors in the first place, not having to specifically go make an exterior waterproof liner look good as well saves them money. If looks don't matter, you're back to the Tyvek/Polycro high viz setups that look hideous but generalize the yellow banana Aerostitch that no one buys by accident.
Performance (corollary: fatigue): There's a few materials you can make waterproof gear out of, and the easiest ones to work with tend to catch wind. By sandwiching the waterproof liner between the mesh exterior and the rider, it won't be flapping in the breeze. This applies to sporting gear too, where puffy gear catches the wind. One thing to consider is that performance and fatigue are often hand in hand conversations: The things that make a bike go fast are also the things that will make it go far. By being "slippery" aerodynamically, a bike will go faster, but it'll also use less fuel. By being "slippery", it will also generate less force on the rider, leaving them with less fatigue at the end of the day.
If you look at high end bicycling gear, it follows similar conversations, except an abrasive resistant exterior is not applied. As such you end up with needing to care for the gear a lot more, like applying Nikwax more frequently to waterproof the gear over and over as any abrasion (including wearing a backpack) will make it less waterproof.
I like the "heavy duty waterproofing goes on the outside" for a different reason too though - as you say, the mesh gear adds a layer of air, which is a substantial portion of what makes puffy insulated gear warm. If the price is right, e.g. polycro or Tyvek, and the performance degradation isn't too high, then that's my go-to choice. For low speeds, it works out well, but when we were doing the big CDT ride, I had to move the waterproof lining inside the jacket because I was catching so much wind it was dropping the top speed of the bike down several mph - enough that safety was compromised.