We have two options where I work. Buy through the corporate 'preferred supplier', which is some travel agent nobody's ever heard of, or buy the ticket yourself and claim it back of expenses. Departmental budget holders are explicitly clear that as the travel agents seem incapable of booking anything other than an anytime ticket, and as they also charge a hefty commission they prefer (i.e. require) staff to buy tickets at their own expense and then claim back. Strong emphasis is placed on making advance or off-peak bookings wherever possible. In all cases the original travel tickets must be retained. Apparently while email receipts do indeed contain all necessary information (origin, destination, ticket type, price, etc.), they can be quite easily tempered with (compared with rail tickets which, relatively speaking, are not so susceptible) and don't meet the strict accounting / auditing standards demanded by the research councils which fund a great deal of my employer's budget (although I am very glad they no longer ask for the reservation tickets on the seats to also be provided, which made travelling to London with Virgin very difficult indeed).
To be quite honest I don't really care about the logic of it all. All I know is that unless I present the travel ticket I am not getting my money back. As it is my employer that is paying my salary, and as it is my employer that will determine whether I am to be reimbursed for work travel, I am minded to follow their instructions.
When travelling for work I always hold on to my ticket and never put it in the barrier. Save for a couple of occasions this has been fine and accepted with no problems. On the couple of occasions I was told I might be tempted to commit fraud or re-use it (despite there being no evidence to support such a stunning allegation). I explained I was more than happy for them to mark the ticket in such a way where the key information was not obscured and all was fine. There was only one occasion where I was forced to put the ticket in barrier, being informed the correct procedure was that once it had gone through the barrier a gate line assistant would then retrieve it. This was London Victoria station at 0845 so you can imagine the chaos that ensued and how incredibly stupid it made the gate line assistant look.
While the ticket remains the property of the rail industry, there are no real credible reasons why it would want to hang onto a used ticket (unless, perhaps, it wants to retain it as part of some sort of investigation, which I doubt anyone travelling on business expenses would have cause to warrant). And if it were so concerned about people committing fraud or reusing tickets it would make more of a concerted effort to carry out on board checks and to mark tickets as used in an appropriate manner rather than relying on gate lines.
Anyway, the barriers at Crewe are rather odd indeed. They either reject absolutely everything or they accept and swallow absolutely everything (including season tickets and the like). Perhaps this is why they seem to be kept open more often than not when I have observed them.