1. Accurate course - you are right there. No excuse for a course to be anything but what is advertised.
2. Well marked - same thing. No excuses there.
3. Port-a-johns - very expensive. They can range between 250 and 350 each depending on delivery, location, quality. The vendors recommend one port-a-john for every 200 people (not joking) which is why there are usually so few. Race directors will skimp on this because of how expensive it is.
4. Extra mat - have to talk to the timing companies on this. An extra mat is a very costly expense. Depending on the number of runners, this can go upwards of 500-1000 for a simple short race. It can cost upwards of 5000 for races with a higher number of runners crossing over it at the same time.
5. Water - pre,post,during - is cheap. Gallon jugs are cheap. You can usually get a grocery store to donate, so I am with you there.
6. Awards timing - difficult because you usually want to wait until everyone has finished and that can take a while. Depends on the distance of the race. For those who finish up front, usually you can just go for a 3 mile cooldown, stretch, and things are just about ready to go by the time you are done. If you really need to stick around for that local road race prize .... then .... be respectful of everyone you beat that day.
7. Awards quality - little known fact that trophies are so frickin' cheap that you can get generic ones for little money compared to other awards. Hence why race directors love them. Custom made usable items are VERY expensive. $50 each or more for a towel if you are only ordering so many.
8. High cost - these days, thanks to the various amenities that runners "expect" like finishers' medals, electronic bib timing, food/beverages. It adds up. Police will tack on numerous details because of safety. Those are very expensive too. You'd be surprised how much of a $30 5K entry fee actually goes to the race, compared to the costs.
9. Methods to catch course cutters (other than mats) - yes, agreed. volunteers are free and a smart race director knows where to place them on the course.
10. Slow runners starting up front - fixed by an announcement at the start for slower runners (KIDS!) to move back. We use pace-signs.
11. "Comped Elite Bibs" - Most of these local races are for local charities and the goal is to promote the charity, raise a small amount of money (less than $25K), and host a fun event. If you are really "elite" then you'll understand why you asking for an elite bib is a little off-putting.