Update: I just set up an MCL2AV (Type 2032, SW2.3) with just power supply and IR transceiver connected (no other input or output as these are not required for a simple test).
With BL5000 (set to two-way control for both AUDIO and VIDEO), full two-way IR volume control is possible (i.e the BL5000 display shows the numerical value of the volume, changing as the button is pressed). Also, pressing STATUS will show the selected source A.TAPE or CD depending on whether SHIFT RADIO 6 or 7 has been selected.
Pressing SOUND toggles between just VOLUME and LOUNDNESS, the latter of which can be turned ON/OFF using the up/down arrows with the display showing new status. (There is no display, nor control, of BALANCE, BASS or TREBLE)
EDIT: So it would seem that 2-way control is possible - but maybe only with my MCL2AV Type No and SW version, plus the fact that it was not connected to a full masterlink system. Also, when you initially used the BL1000 and pressed SOUND twice followed by arrows, you were possibly turning the LOUDNESS on and off, hence noticing the slight change of tone.
EDIT2: And surprisingly most of my BL5000's display has started working again - must be the warm weather:
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