Yeah, the MTU is a lower level. It does affect throughput, though. For example, a UDP packet that exceeds the MTU is more likely to be dropped/lost since ethernet has to reconstruct the full packet on the other end. So while 100% of 100 byte UDP messages might get there, statistically it’s very likely that many 32k UDP packets get lost.
…but most of us shouldn’t worry about that most of the time.