First - Title of Flat is not clear. It has to be made straight then only you proceed .
Second - myself also suspicious like above advocate , Stamp Duty is more and Registration fee less then why this person did not get it registered . On the contrary as per understanding or some old information (Not sure 100%) time which you state , that time registration was allowed even if stamp was less or some issue regarding stamp adjuidication pending , So few cases matters I saw where after registration the office send notice demanding more stamp dues. So this transaction seems to be suspicious or not properly done .
Third - When Suspicious things are there , My habbit is to check every thing in dept , because it requires further minute microscopic examination of title and property.
Fourth - There are provision by which we can make straight previous title then transfer the flat to you, but this thing require proper documents and every thing analysis . This forum is too short. And If I start explaning then I have to write book here how to examine the title of property and various complication regarding them . So better contact some good advocate practising in property law.. You need to check every thing from land to every thing regarding this fresh.
Fifth -- If you had come to me for title certificate of this flat , I would have denied it to give till exhaustive study . Generally Title certificate is required from expereinced advocate that he states all the points what he have examined and concluded that titile is good and flat can be sold.