The situation what you have discussed here is not the law of the land, this may happen in some places and not everywhere.
Assuming that an event similar to what you have described here, if you go by the advise received to receive the excess amount beyond the sale consideration amount through bank transaction itself, the amount received through bank cannot be denied hence you can show the excess amount as income from other sources, and you don't have to specify the other source in the ITR.
Firstly you make sure that the registration of the property is executed by the buyer paying the actual, sale consideration amount shown in the sale deed which may be more than the government guidelines value, if the Sub-registrar is denying to register the property to the value higher than the government guidelines value, then you can approach the District registrar with a complaint against the sub-registrar and seek his direction to the sub registrar to register the same as per the value paid by the buyer which is the prevalent market price.
If you do not want to take this trouble then you can think about the alternate option as suggested above.