The fliers are all booked to use the fast lines at least as far as Radlett Junction, the only exceptions being some that stop at West Hampstead or start all stations running from Elstree. If everything runs to plan, there should be no disruption to MML services, the time you get MML services held up is if the Thameslinks are late, or if the MMLs are late and out of their slot (running behind a flier that they should be infront of). The fliers have quite a bit of slack through London to try and gain back any delays on the Southern section before joining the MML, and it's not uncommon for them to wait a few minutes at Carlton Road or West Hampstead South where they join the fast lines. If fliers use the slow lines they are unable to overtake the preceeding Metro, so will end up delayed, and also suffer from the lower lines speeds (slow lines are mostly 90mph, but there are a lot of slower sections where they diverge for stations, tunnels and Silkstream Junction). Quite a few fliers are booked to use the fast lines beyond Radlett, crossing over at Harpenden, Leagrave, Flitwick or even Bedford. Some of the fliers are booked to run limited stop beyond St Albans, missing out LAP, Leagrave and Harlington. Similar arrangments, where the semi-fast suburban trains share the fast lines with the express services for some distance, particularly on the none stop part, are found on other lines aswell.
