When archaeologist classify there finds and when they try to understand its function they take recourse to many steps and one of it is trying to understand the function of the finds with its similarities in shapes with present day things.
One of the foremost reason of doing this is because many reconstructions of Harappan civilization are made on the assumption that later traditions provide parallels with earlier ones. This is because archaeologists often move from the known to the unknown, that is, from the present to the past.
For example there are evidences of pottery, tools, ornaments, households object etc. We can easily deduce its function because the shapes resembles the present day objects. There are also evidences of toy carts, boats found from Harappa whose function can be known because of its resemblance with the present toys of the children.
Although such thing's function can be easily deduced the main problem the archaeologist face is when they try to apply same methods to reconstruct the religious beliefs of the Harappan people. For example The Proto Shiva seal and the various cones of small size made out of Lapis Lazuli, jasper etc, this things when looked looks like the present day objects hence they are given named like Proto Shiva and Lingas respectively but it is mere speculation, there are possibilities tha seal could be depicting a Shaman or someone else and those cones could be just cones used for board games.
For example The Great Bath at Mohenjo daro, is believed to be a place for bathing for ritual purposes because there are such places here in India. However we are not sure if it was use for such a purposes during that time.
Hence, the method to look for the present day resemblance in the object is useful when the objects are obvious as in pottery, jewelleries etc but it becomes tricky when same methods are applied to understand something else like beliefs, religious practices etc.