PLovett,
First, may I qualify my comments to be unrelated to any specific accident, incident, or modification.
Confining my remarks to Oz (I see that you are so located ..) .. and presuming that your comments related to Oz observations ...
The intention in the certification process is that the TP certification fraternity make assessments and adjudicate on the acceptability of pilot station layout. It follows that, for modifications affecting flight station layout, the same folk should be involved in assessment ..
For many years in Australia, however, that assessment task has been delegated routinely to the flight standards examiner folk (regardless of whatever evolving titles they go by). I suggest that the reason for this is that the Regulator (likewise) has never had other than a minimal (usually one) TP on staff with the result that the certification TP only has had time to be involved with the more significant mod programs. I note that I have been out of the modification design game for several years so my comments should be seen as historical and may not be totally correct for current circumstances.
The results of flight station modifications have been mixed, to say the least.
I am not suggesting that the good flying folk are not competent - quite the opposite - however, in the main, their competence lies in flying and flight standards assessment rather than design and certification things.
As a consequence, in Australia at least, many aircraft modifications have been assessed as being satisfactory from the viewpoint of flight station layout when, probably, the certification TP would have given a different assessment ....
Two anecdotes ..
(a) I had a lengthy technical discussion with the relevant TP colleague in respect of a mod which had a nav display in a not altogether desirable location .. the cockpit was sufficiently busy that there was just nowhere else to put the thing .. we eventually agreed that it was OK to leave it rather than redesign the entire forward panel to put it someplace else.
(b) on a single seat endorsement years ago, the ASI was located up on top of the coaming (interesting location I thought and possibly desirable for the air ag community) .. endorsement was done one afternoon so that I could go towing the next day .. cloud base lower (?) than desirable for an endorsement ... I was quite alarmed for a few seconds when the thing leapt off the ground in about 100 ft and I couldn't find the ASI (under stress, of course, looking to the "normal" location) .. never a good thing to let oneself get behind an aeroplane ..