Couple of other points which look like poor design. Para 18 states that when a loco is coupled at each end of the train, there could be "damage" to the jumper circuits. Yet dividing at Carstairs like this is part of normal nightly operation, and indeed normal railway operation. It was just never envisaged at the design stage, or in the test plan, and then led to an issue of an e-mail instruction which actually contradicted the Rule Book requirement to do the brake test last; so much for all the checking that's meant to go into such procedures. There's also a sly mention at para 123 that the closed position for the cocks was down on the coaches and up on the locomotive, and the coach cock has now been inverted so they both point the same way. That really is industrial design 1.01 to get right.
I'm uncertain as to why you've seized upon these particular points nor why you consider them to merit comment. It almost feels as though you've some point you're trying to prove.
The part of the coupling operation that could cause damage is the connection of the 61 way jumper cable. The reason for avoiding having two locos connected simultaneously should be fairly obvious, as connecting a second loco effectively connects a second power supply to all the circuits on that jumper which introduces the risk of damage due to an overload. As these circuits could include controls for the doors, PASSCOMs and other safety equipment, it's clearly of great importance not to expose them to avoidable damage.
In this regard the Cally Sleeper's Mk5s are no different from a lot of other stock where similar care needs to be exercised. For example, before "keying in" on a Voyager you must check on the TMS that there are no other keys already in, as having two keys in simultaneously causes an overload in the control circuits requiring the attention of the fitters. Checking that there are no other keys in forms an important part of the Voyager pre-coupling checks for the same reasons. But before you cry that this is simply a post-privatisation issue, similar problems could affect ex-BR stock from the pre-microprocessor era. It was always drilled into us when learning Cl315/Cl317 EMUs that it was very important that you took your door key out when you left the cab. If you accidentally had two door key switches live on the same train the resulting overload could fuse the relays which could cause some serious wrong-side door failures. Again, this meant a call to the fitters and the unit(s) being taken away for checking. All of these things can be (and are) mitigated by ensuring that the procedures are clear and that the necessary checks are made.
Besides, the only reason why the 61 way connection is mentioned at all is that the need to avoid having two locos attached at the same time necessitates that certain parts of the coupling and uncoupling procedures need to be carried out in a certain order. I'm not even very sure that it was particularly relevant to this incident as it seems that it was the second ETS connection, the shunter's inability to safely make it at the first attempt due to a freight train on the adjacent line and the subsequent difficulties in connecting it that were the main issue. But this has now been addressed by changing the procedure such that the loco already attached which hauls the Glasgow portion draws it's half of the train forward permitting the loco for the Edinburgh portion to undergo all the various coupling operations in one single go, including the 61 way jumper cable, which should remove any confusion about what needs to be done when while the loco is coupled.
The direction in which the handle of the BPIC faces really isn't such a big deal. On any individual train there will be cocks facing every which way, and often cocks with different types of handles, but this poses no great issue. As with all other devices of this type, railway isolation cocks follow the global operational convention meaning that it is obvious which position is "open" and which is "closed". Rather than belittling the level of engineering you might have highlighted the rest of Paragraph 123 which explains that reversing the position of the BPIC handle also introduces a failsafe, in that an unlatched BPIC handle should vibrate into the safe (open) position.
I think you also either misunderstand or misrepresent some parts of the report. You assert that the 61 way jumper resulted in an instruction that meant that the brake test was not done as the last action, in contradiction to the Rule Book requirements. This is not true, as the Rule Book did not mandate that the brake test should be the last action at the time of this incident. In fact it still doesn't. The RAIB have only just recommended that the RSSB consult on having this explicitly stated in the Rule Book (Para 127). The requirement as it is stated in the Rule Book at present is that the brake test must be carried out when the loco is coupled, and at the time the brake test was carried out the loco was coupled, even though there were still electrical connections to be made (Para 76).
Isn't having the EP brake and air brake combinations all on one locomotive just what Class 73 (a 1960s design) long had, locos which handle other sectors of the Scottish sleeper operation.
I think I'd just like to clarify this point. Yes the Cl73s (and Cl33/1s) had an EP brake, but this was to permit multiple working with SR EMUs and push-pull working with TC sets. Hauled dead, even by a Cl73, an SR EMU would be worked as a conventional two-pipe train.