The MSX Technical Data Book references the CLK on the slot as the CPU clock, also says the speed because at that moment it was fixed... So, I think that Panasonic took the easy way to keep compatibility with old cartridges that rely on the clock speed being 3.5x.... But since it is meant to be the CPU clock, if the CPU is driven by a faster clock, the correct approach would be to have the faster clock there... At least that is my interpretation, of course, that causes issues because since most (if not all) MSX machines had 3.5x CPU clock, interface designers might have took the assumption route that it would always be like that... 
You can’t have an external bus with unspecified maximum timings, and expect it to be backwards compatible if you increase the speeds. That would not be a robust hardware interface design. Cartridge manufacturers can’t be expected to make reliable hardware under such conditions. So it is entirely reasonable that the cartridge slot timings are specified in terms of a 3.58 MHz Z80.
The turboR takes the correct approach by keeping the timings within original specifications when the cartridge slot is accessed, that is, both the CLK frequency as well as the timing of the signaling of RD, WR, IORQ, etc. Because the internal memory is accessed at full speed, the performance cost of slowing down the external bus access a little bit is quite minimal, because external access is comparatively rare.