I asked them on their forum, a few months ago, this exact question. Below is their response...
With the DAT file [from Maxmind], you cannot do grouping (group by city,region,country), select IP by country (where country_code = 'US'), modify the data (eg : change country code from ISO to FIPS standard), join with other SQL tables and you can only do queries one at a time... Some people might not have access to the server (eg shared hosting) and the MySQL DB could be the only way they can install it. Also, some develloper might prefer using the data in a MySQL format because thats what the application they are running is using.
There is a few extras such as IP CIDR by country and I might add timezone soon.
That one comes in a small binary file that allows to avoid even using a SQL DB for the lookups (faster for some people + easier to manage)