Samrat knows how Sai feels about virat-pp very very clearly!
He knows that the only reason that Virat even revealed the issue of meeting pp in cafe was because Sai saw them there. Samrat knows about the hand holding too. But he believed his brother and took everything Virat said at face value because he has known Virat as a righteous guy.
however he knows that Sai is having a tough time coming to terms with virat-pp past and believing that virat is truly over pp. Samrat can relate to this - because he knows how it feels to have your partner have a past with someone else. But he is more experienced n mature and he could see that Sairat had a special connection - they cared deeply for each other n they could be good for each other- thats why he tried to counsel Sai to look at her relationship with Virat through a different lens. But now, Samrat is starting to see exactly WHY Sai has been so hesitant, wary and resistant to believe Virat-pp- its because of how they behave with each other despite claiming to be "over" each other. Virat allows pp to speak in between him n Sai ALL the time. Pp attacks Sai repeatedly , relentessly, mercilessly and garners support from elders of house too n she shows just too much interest in Virat even now despite claiming that she wants to move on with him.
Right now, all Sai wants is to peacefully exit the CN. What Virat/pp/Samrat do is their business.
Yeah virat himself can't see how his behaviour with pakhi, and his biased behaviour between pakhi and sai only makes sai believe more that virat still loves pakhi, but samrat has picked up on this as he has witnessed not only pakhi interfering in sai-virat's matters, filling virat's ears against sai instead of trying to de-escalate situations between him and sai or talk sense into virat, her looking for ways to insult sai, but also how virat too lets pakhi do all this without reprimanding her or telling her not to interfere between him and sai, as well as virat even joining pakhi in taunting sai. To Samrat It looks very wrong the way pakhi and pakhi-virat both are behaving with sai; the same reason why sai too still suspects virat hasn't fully moved on from pakhi.