Muralidhara's version of Krishna and the cowherd boys with the Gopis watching them shown in the lotus is nice. Krishna and the cowherd boys used to return in the evening, and the Gopis while looking on used to enjoy Krishna's smiling face. This is stated in Srimad-Bhagavatam.
Regarding whether the Brahmajoti should be painted rainbow colored. It is our experience that in the material world when the sunshine is very bright there is not any color, just whiteness. Colors of sunshine only become manifest when there is a tinge of clouds. So in the Brahmajoti there is no possibility of material tinge. So how it can be rainbow colored? In the dazzling light there is no possibility of colors. Considering all these points, Muralidhara should paint maintaining the artistic sense as well.
The Mahattattva may be shown underneath the lotus if it is required for design purposes.