One goal is to get the likes of City and Chelsea to change their behaviour and stop injecting cash freely into the transfer market and making huge losses.
So far they've already changed their behaviour by trying to conceal a proportion of their cash windfalls in faux sponsorship deals.
Take City's 400m Etihad deal which is exactly one of the deals set to fall under considerable scrutiny (to which this UEFA threat refers):
http://www.independent.co.uk/sport/football/premier-league/citys-400m-etihad-deal-improper-says-euro-report-7544605.html
"In order to avoid improper transactions of this kind, Uefa should prohibit clubs from sponsoring themselves or using associated bodies to do so. There is also a need to monitor the 'purchases' of sponsors, who should not overpay for the rights they acquire."
If a rule of that nature is needed, it can be implemented and enforced even if it doesn't end up applied retroactively (although according to what I know about FFP, it already has been implemented, and can be enforced now).
And if UEFA's auditors decide that the real value of the deal is 200m (and let's say the real, real value is 150) then City will be forced to give up 200m and the current situation in football as a whole gets somewhat less insane.
There is plenty of legal precedent for reviews of whether sale value matches real value. Occurs all the time in insurance, property settlements, M&A etc. There are whole branches of industry devoted to the problem of valuation.
The other goal of FFP is to stop financially weak clubs from scuttling themselves with outlandish spending they can't afford. That ought to work very effectively if similar rules are implemented at domestic level.
Football is big money but it's nothing compared to, say, BHP bidding on Potash. No matter how much money is involved, there's an army of lawyers, accountants and assessors on hand to help police it.
