After spent some time unsuccessfully looking for precise information about the Mouse protocol used by MSX computers I got a subrom binary to disassemble and take a look.
Mouse reading is performed by NEWPAD subroutine at address 0x1ad but the reading effectively occurs after addres 0x3509:

The Mouse routine reads 6 nibbles (0..5) in sequence, cadenced by the (toggling of) pin 8. Delay loops are inserted between readings .

The routine may end by updating the X and Y displacement coordinates with either the packing of nibbles [1.2] (XSAVE) and [3.4] (YSAVE) for a Mouse or a signal extended nibble [0] (XSAVE) and nibble [1] (YSAVE) for a Trackball.
Either one or another possible subroutine ending depends upon the value of the last nibble read (nibble 5). I stll have to figure out how exactly does the code below works
Values 8 and 9 will return as a mouse. Remaining values will return as a trackball.
.... xor 008h ; invert bit 3 of nibble 5 sub 002h ; ? cp 00dh ; ? jr c,returnMouse ; return mouse ; returnTrackBall: ....
I haven't found information anywhere about the purpose of the brief positive pulse issued after all nibbles are read.

So are we talking LSB or MSB nibbles here?