Interesting question! I had not considered it before. I think the meaning of modulate that applies, from my concise OED, is '2: vary the strength, tone, or pitch of (one's voice)'

Emma might be saying Robert Martin speaks in something like a monotone, rather than having more musical and pleasing ups and downs (variations of strength, tone, or pitch) in his speech. But it could also refer to his simply speaking too loudly. Perhaps as someone who is so much out-of-doors, he has never learned to tone down the volume in the parlor (or she imagines so).