I work for a major corporation (80,000 employees worldwide) but have a job that requires 60-80% travel so I have some flexibility that others may not. I'm a senior technical advisor so equivalent to mid-level management from a seniority/payscale perspective.
Our corporate portal is quite good and there are some tricks. It flags your itinerary if your chosen fare is more than AUD 140 more than "lowest logical" for domestic or something like AU $350 for international. This wiggle room allows you to avoid totally stupid options usually, and allows me to choose my airline domestically in most cases. How it determines "logical" is based on what you specify as your required departure and arrival time, which you can make as precise as + or - two hours. So if there's a flight you want at say, 9:30 am and one you don't want at 10:00 AM, you put your departure time as 7:35am and +/- two hours, which means it won't find the 10:00 AM flight in the filter. It also generally allows you to pick nonstop over connecting without an issue even if the fare is considerably higher. Even if I need to book something that gets flagged, due to my job role and travel experience I'm allowed to book anyway with the flags reviewed later by a travel manager (others have to get explicit approval for deviations). I've never had a travel manager say anything so I guess I haven't done anything too egregious.
For most flights I typically do "red e-deal" (or sale) on the outbound and Flexi on the return, but this is mostly subject to whether I can do this without causing too much trouble with the lowest logical rule. The company would prefer lowest fare all the time, and if you do have to change, just eat the change fees - this often is way less than Flexi fares. I would go along with this but sometimes need a few extra SC's... please don't tell on me
It's all Y by default, of course, but frequent travellers get a special exception for PE if the itinerary is 14 hours or longer (combined flight time of all flights, not including layovers). The problem with this is that the portal recognises US airlines like United and American with their "Economy Plus" or similar products as PE. These US airlines all have the same seat width as Y in these products. I refuse to fly 3-3-3 in a 787 on United, even if it is a bit of extra legroom when I can fly the longhaul on QF in economy on an A380 in the upper deck with plenty of shoulder room. Qantas PE is extremely expensive, something like $3000-4000 more and this would be hard to explain. So I've actually not "used" this policy on my US flights. It does come in handy when flying to Europe or Asia if you can hit that 14 hr minimum (which is hard for Asia). There is more competition for "real PE" in these routes and hence the upcharge is more reasonable, plus you don't have the fake PE of the US airlines to worry the portal comparing against.
Overall I'm happy with the policies, it seems a good balance of frugality and flexibility for travelers. The self service approach does require you to be savvy about travel booking though - not all of my colleagues are as happy about figuring out the ins and outs of our portal.