MBT

Hello, if MBT is achieved from let's say, 95 octane fuel, will the use of higher octane fuel be for nothing?

The engine is going to be knock limited in at least some areas. In those areas, you will benefit from higher octane fuel (higher RON pump fuel or switching to higher ethanol blend). As a very simple example, if I can run MBT at 3000rpm and 50 kPa boost (~150 kPa manifold absolute pressure) on 95 RON, I can run MBT at maybe 70 kPa boost with 98 RON.

And what if taking into consideration a naturally aspirated engine?

Naturally aspirated are still knock limited, but it depends on compression ratio, valve timing, cylinder bore size, motion inside chamber due to head design, and residual gas due to exhaust manifold design. At low rpm (say under 2500rpm) they are more knock limited than high rpm.