AFAIK,RCS depends up on the surface area. But for spherical object,the reflection will be spread towards the radar receiver irrespective of the angle between the wavefront incident Radar. But ,for angled surface reflection will have directional property. Since u have designed the aircraft,you will be know at what angle the radar wave reflect with respect to the scanning Radar.Yes, I agree that the rectangular shape is better for stealth compared to the spherical shape. I don't feel any measure modifications are necessary to contain the IRST and EOTS inside a box. If changes are required, ADA will do the needful.
IRST will definitely increase the overall RCS, in case of F35,the glass panels are almost parallel to F35's fuselage angle. So the reflection contributed from EOTS will also parallel to the F35's fuselage.
It's no brainer, of you are designing AMCA asper the model shown in post#1117 ,then it will be a compromised stealth. And I am damn sure that our electronics cannot negate the effect of compromised stealth,we are not as advanced like French to do what they have done in Rafale.