I think in Jet2 you can't apply to be a senior first officer without having your ATPL and that does come with a pay rise. So a financially penalty if you miss it. Other airlines may have the same deal.
Ryanair (well there was a rumour) in Ryanair that they tried to do all ATPL upgrades in your command upgrade sims so that you would not bugger off to another airline as soon as you had it. This I believe was horse poo but you never know.
All is my own opinion and subject to been 100% wrong.