Warranties are contracts and hence if you breach the rules they are normally voided. The main purpose of the block exemption was to deal with competition issues - specifically forcing drivers to use main dealers and expensive "genuine parts" or risk voiding their warranty. Instead it provides for non-franchised repairers to use parts manufactured to an equal quality. The requirement is normally that the service is carried out to the standards the manufacturer requires and also at the recommended interval.

Generally speaking, I would expect a missed service to void any warranty from Kia. Furthermore I believe Kia's extended seven-year warranty has some additional conditions which does require authorised service agents. Hence while a three-year warranty might be covered under the block exemption, if you want the Kia extended deal you need to jump through some additional hoops to get it. Honest John himself may be able to advise further as to whether this is the case.