I prefere the MK basses for the very same argument you like Yamaha. I don't understand onboard electronic. IR and simulations are evolving so rapidly that the onboard Yamaha electronic might age faster than the bass.SLB vs MK, it's a buy one cry once scenario. I think that yes the MK has a lot to offer for the price. Back when it was SLB200 vs the MK, it was a tossup and you could argue that you were getting a much better looking instrument in the MK. Either is not beautiful to me (nor is the SLB300). They all look like big crossbows.
With the SRT technology, the SLB300 is far more compelling. EQing helps with making the tone sound like a real UB than the former, but none of that can add resonance. In some rooms and venues, the lack of resonance is less perceptible. However I personally wanted to benefit from technology that solves the problem I've always had with EUB's. If you're going to buy a new EUB today, it makes no sense in not having this feature that makes a huge difference in sound (pun intended). I've heard people trying to use an MK or SLB200 + ToneDexter +EQ , but in the end it seems like a lot of effort to try to get a bass to do exactly what the SLB300 does right out of the box.
I do have an MK and I'm using it via a 60$ Nux Mighty Plug with IR and cab-sim and it sounds very good. I could buy extra IR too but I didn't bother at the moment.
Yamaha are almost twice the price of am MK Studio and IMHO the difference cannot be justified by the electronic package.