Eray,
There are multiple examples (more than I can enumerate) of Class 3 Board-In-Board applications.  The requirements of IPC-A-610, in lieu of an established standard, is an AABUS (As Agreed Between User and Supplier).
Typically, you will only be soldering on 1 side, so the fillet heights, registration % and other requirements need to be established.  If you are using Butt connections, Butt connections are Class 2 only and must be exempted as part of the documentation.  The biggest concern with Board-In-Board is not stressing the solder connections, so you need to evaluate the support method for the mounted board(s).  Most applications I have dealt with involve some sort of slotted shield or other support grid, or for commercial applications, I use a RTV application to stabilize the mounted PCBA.

I am guessing that the design is using Board-In-Board to overcome 1 or more of the following (non-exclusive list):
The height added by using card edge connectors, the impedance/capacitance added by card edge connectors, to reduce overall cost by eliminating the need for card edge connectors and gold fingers, or improved reliability as the mounted PCBA cannot become dislodged from a connector system.