I'm currently rollin on Koni's on my '99 SVT with no mods. You might be mistaken with those who run Koni struts with coilovers; in their case they have to modify the spring perches on the strut so that it will fit inside the coilover spring.
1999 SVT
removed res
FMS 9mm
metal impellar
Koni struts
PG Xenon 6.5
MSDS Y-pipe