From a company’s perspective, they are buying an asset (the bike) and renting to an employee. As long as the company recovers all monies from the rental and final payment (and associated employers NI payments) and is cost neutral for the business then they should be OK. From an audit front, it has nothing to do with them – its the businesses asset to do with as they see fit.
With regards the final payment, again, the business can charge you what they like, nothing to do with HMRC. What HMRC are now doing though is stipulating what they perceive the value to be. So, if you make a final payment of £50 when HMRC are saying fair value is £250 you will have received a benefit in kind of £200 and have to pay the tax/ni on this.
As Fuzzy says, a way to reduce this is to delay the transfer of ownership for a couple of years so the fair value reduces.
There are still decent savings to be had if you self administrate – you just need to run some sums to work out the savings. I got a 2012 bike reduced from £1050 to £800 on our scheme. I reckon I’ll end up paying just shy of £500 for mine so worth doing IMO.
A couple of threads about this here
http://singletrackworld.com/forum/topic/talk-to-me-about-cycle-to-work-scheme
http://singletrackworld.com/forum/topic/cycle-to-work-scheme-12