I actually came up with a few thought on this one.
First is bloom contribution. Not sure where I was going with that one, but I'll let it percolate.
Second, is per-Mission flags/setup for Light Shafts. Right now, it's either globally on with a static set of values, or it is globally off. That doesn't sit well with me. Places (in FRED) that it could go is either in the Mission Specs or the Background. Mission Save should have 2 lines (or maybe just one) defining "$Light Shaft Flags:" to indicate that it is on (if one liner) followed by comma separated values for each of the control values in the order as listed in the Post Processing Table. Would still only ever take effect if -post_process is present, but also won't care if the TBL cites them as "Off" (which means then that most mods won't have to distribute one -just- for Light Shafts).
This will not only allow for better instancing so that it doesn't have to be on for missions that don't really -need- it, but also allows significant control over how MUCH there is.
And now I remember where Bloom Contribution comes in. Add as an expanded value to the existing Light Shafts setup a Bloom Modifier that controls (either in two parts or one part) how much (if any) contribution that the players Bloom setting will affect.
Additionally, could expand or tie in the Light Shafts to the actual Suns listings so each Solar body has an element of control for its respective intensity and type, but that may be much more complicated than just a stock per-mission, but would probably be much more ideal.
In terms of the general corona/glare contribution to the scene, that can happen even without -post_process and Light Shafts and could probably use some toning down or introduce some controls so that mission designers can better control the intensity and contribution thereof.