Black/silent video with specific duration with ffmpeg
Specify a PCM codec. The default codec is AAC, which has a priming sample that format in ffprobe accounts for, but stream won't, since the demuxer will have discarded it before sending it to the decoder for analysis.

P.S. your syntax is wrong - it should be ffmpeg -f lavfi -i color=c=black:s=3840x2160:r=25/1 -f lavfi -i anullsrc=cl=mono:r=48000 -c:v h264 -c:a pcm_s16be -t 3 out.mov

Options before an input are applied to the input. You've gotten away with it because -c:v h264 sets the video decoder for the following input. However, since it is an audio-only input, the effect is inert. And the default codec for MOV happens to be H264, so the outcome is what you desired.