A few observations:
1/ ST is a concession, not a benefit. Making an issue of it will only attract the attention of HMRC. Following a legal route to prove it is contractual only opens the door to retrospective tax assessment. Even making HMRC aware of it may cause more investigation of its tax status. Outside of the airline industry, within the UK, HMRC seeks to ensure that any subsidy for commuting is a taxable BIK.
2/ To suggest that any case within a disciplinary procedure should be set aside (assuming that such a disciplinary procedure complies with the ACAS code of practice) as part of any IA settlement is nonsense. justice must be seen to be done - if there is no case to answer, or unprovable, the "accused" walk free. If there is a case and the accused aren't satisfied with the result, there is a statutory framework to deal with it.
3/ The nominal reason for the IA is imposition. I understand that any further IA based on the above two issues would require a new ballot to be instigated (not an online poll as suggested by BASSA)