I suppose if intonation COULD be altered by such things, we wouldn't be getting so hot under the collar over sawing up endangered hardwoods....

😎

Sadly though, and my interpretation of intonation is similar to everyone else's here, it can't really. However, if certain harmonics that were damped at saddle / bridge level are now passed into the guitar top, then their ference / interference with other harmonics and indeed fundamental waves may well colour the resultant sound differently. If you want to call that intonation, I'll not put my tanks on your lawn.