Welcome to Yamaha Synth! Great question...

The "Scene" is a Yamaha innovation that, as implemented in the MOXF, memorizes 12 different parameters... some are Sequencer settings, and the others are Tone Generator settings. This type of memory is called "snapshot" - a term that comes literally from recording studios back in the 1970's; before the invention of AUTOMATION. Every recording studio back then had a Polaroid SX70 camera - you know, the kind that had the special photographic paper in the camera, you took a picture and it spit it out - and in about 3 minutes the chemicals on the paper would develop the picture right before your eyes! The snapshots were used to take a picture of the EQ settings on the mixing console, the cables in the patch bay, the Fader positions, etc., etc., so that you could restore your settings at your next session. The photo was placed in the box with your 2 inch tape. (truly analog automation) Next time that band was in the studio - you recreated the mix from that snapshot.

"Snapshot" memory is literally a way to memorize the important settings - what Yamaha has done is take certain important settings and capture them in an instantly recallable memory location. There are six SCENE locations [SF1]-[SF6]. These can be automated on the Scene track or manually recalled when needed.

The SONG (sequencer) parameters are TEMPO, TRANSPOSE, PLAY EFFECT and TRACK MUTE:
TEMPO
While there is a dedicated TEMPO track, Tempo is one of the parameters that is memorized by the "snapshot". Of course, you are not limited to just six tempo changes, you can insert a tempo change at any time in a SONG (as it has a dedicated Track just for tempo changes).

TRANSPOSE
TRANSPOSE - you can OFFSET the Notes being played from the Sequencer, using the TRANSPOSE parameter on the main SONG screen. Yamaha implemented this so that all Tracks with "Normal" Voices assigned will be offset according to this parameter. Any Track with a DRUM KIT VOICE assigned will not Transpose (why? Because drummers do not transpose, it would be a disaster as they would start hitting the wrong drums, so it is an 'intelligent' offset of the pitches.

PLAY EFFECT
Any Offsets you make using the GROOVE GRID (the Play Effects) can also be memorized in the 'snapshot'. These as you know, can be "normalized" which means once you apply the offset to "Note Shift", "Clock Shift", "Gate" (duration) Time, or "Velocity", you can have the sequencer write those changes into the track data, and then have the GROOVE GRID reset to zero... The Groove Grid divides a Measure into 16 segments - you can OFFSET any of those 16 segments. By having these OFFSETS stored in a SCENE snapshot you can change up the "feel" at any time. This allows you to setup your own Groove Quanitze. For example, you might setup a GROOVE GRID that changes a straight groove to a triplet feel. Storing this to a SCENE means you can instantly recall a entirely different feel. Or you could take a bass line that was long held notes and shorten the length. By applying this one measure template, you can are really creating your own swing quantize. Of course, if you like to make that change permanent, you can NORMALIZE it - which will destructive rewrite the MIDI event data in the track - then zero out the GRID.

MUTE
TRACK MUTES can be stored in the snapshot, but you are not limited to just the 6. Track Mutes (another Yamaha innovation) was not a part of the MIDI spec, but is very useful. Basically you are preventing the Track from transmitting its information to the tone generator... silencing the musical part. But you can still play the sound from the keys. There is no limit (theoretically) to the number of MUTE EVENTS you can insert into a SONG, as it is a separate insertable event. While there are only 6 Scene memories, you can have as many TRACK MUTE events as you require. These can be inserted manually (to the SCENE Track) or recorded to that track in real time.

The TONE GENERATOR parameters:
All of the other 7 items memorized by the SCENE have cc messages (Control Change) messages that can be inserted anywhere you like, manually, on the track you would like affect. They each have a dedicated KNOB in your KNOB CONTROL FUNCTION area on the front panel - movement of these knobs can be recorded in real time, if you prefer, as these are all standard MIDI control messages.
Pan = cc010
Volume = cc007
Reverb Send = cc091
Chorus Send = cc093
Cutoff Freq = cc074
Resonance = cc071
AEG Attack = cc073
AEG Release = cc72

As mentioned, the MIDI spec does not provide a MUTE event. If you send your sequence in real time, to an external sequencer, it will not document the MUTE Event... but what it will do is record the silence caused by that event turning the MIDI OUT from that Track OFF. So while there is no MUTE EVENT in your external sequencer, the SILENCE that is caused by the track being muted will simply be observed.

Hope that helps.