Why should lower limit of a Control Area (above 3000 ft) coincide with a VFR cruising level?
VFR cruising levels are always located between two IFR cruising levels. With half of the required radar separation minimum to each the IFR level above and below it.
For example:
required separation minimum: 1000ft
IFR lvl: 200
VFR lvl: 195
IFR lvl: 190
The sectors are split at VFR cruising levels to ensure, that both the upper and lower sector can use ALL of their IFR cruising levels while maintaining separation to aircraft that may fly at the highest/lowest level of the sector below/above.
Example:
Sector A is working from FL145-FL245
Sector B is working from FL245-FL355
Sector A may use every IFR cruising level within the sector (FL150, FL160, ..., FL240).
Sector B as well (FL250, FL260, ..., FL350).
As the difference between the highest and lowest level is always 1000ft, separation is ensured also between aircraft flying on top of each other in different sectors!