Built-in protection diodes do only help to prevent latch-up by reducing the probability of occurence. But they cannot guarantee it. If the latch-up protection would always work as intended by manufacturers, then we would never observe any latch-up. But reality looks a bit different...
I refuse to accept "5V tolerant" for the above reason. When I mix a level converter is mandatory

This example may show you that it is not so simple just mix 3V and 5V devices.
When you follow ALL the rules, it IS simple.

To mix devices provided by different supply voltages needs an experienced developer.
I would phrase this as "someone that know the rules and follow them"

Heavier ground bounce of 5V devices demand an ultra clean ground routing management, which in most cases cries out for a multilayer board design, because only this can guarantee the needed solidity of ground plane.
Again, mixing is no problem if you do it right; however, if you take shortcuts such as "I do not need a 4-layer board" or "the inputs are 5V tolerant, no converter needed" or "Voh from 3.3 can drive 5V HC chips" - Look out, it will get you.

Again, mixing chips of different supply voltages can be very very troublesome and should be avoided if possible.
Very often it is impossible to avoid mixing these days, one example is USB that require 5V and most USB chips (e.g. Cy.. SILabs) are 3.3. Also my current favorite el cheapo, the LPC9xx is 3.3V.

The big thing about mixing is "noise margin", "noise margin" and, of course, "noise margin"

Erik