Usually, chakra locations are indicated in the front even though they are actually located in the spine. vibhuti, kumkum etc. is applied on the bhrumadya which is between the eyebrows and also at the -vishudhi_ chakra located at the pit of the throat. Hence, using this practice of frontal location of chakras, the root chakra is fixed at the perineum. Guruji has pointed this more tersely in his comment.
Another reason for using the manipuraka chakra for this purpose is that this is the only chakra where all the 72,000 nadis meet and disperse carrying agni or the energy element to the remaining 107 chakras in the body. Applying energized oils at manipuraka chakra is more effective than at the mooladhara chakra.
