The amount of data taken up by indexes is dependant on the property type
if your properties are ListProperties with a lot of values you will get a very large index overhead, and yes Metadata doesn't include indexes.
Metadata is the overhead your entities incur with things like property names, keys etc... (remember the name, type and value of the property
is stored in the entity)
Just to give you a comparison, in one instance, I have from the stats 455,000 records, 267MB data, 129MB of Metadata
and have used 1.52GB of quota.
So your numbers look about right. Without knowing what you entities look like.
Rgds
T