You can’t set it. FFmpeg choses the version automatically based on the desired output. to force a version, you must use options compatible with that version. Read this link (intro from that page below) and choose the correct combination that works for your application.
Within an MPEG audio file, there is no main header, as an MPEG audio
file is just built up from a succession of smaller parts called
frames. Each frame is a datablock with its own header and audio
information.
In the case of Layer I or Layer II, frames are totally independent
from each other, so you can cut any part of an MPEG audio file and
play it correctly. The player will then play the music starting from
the first full valid frame it will find. However, in the case of Layer
III, frames are not always independant. Due to the possible use of the
"byte reservoir", wich is a kind of internal buffer, frames are often
dependent of each other. In the worst case, 9 input frames may be
needed before beeing able to decode one single frame.
If you need to retrieve information about an MPEG audio file, you
might simply locate the first frame, and retrieve information from its
header. Information within other frames should be consistent with the
first one, except for the bitrate, as you might be retrieving
information from a variable bitrate (VBR) file. In a VBR file, the
bitrate can be changed in each frame. It can be used, as an exemple,
to keep a constant sound quality during the whole file, by using more
bits when the music is more complex and thus requires more bits to be
encoded with a similar quality.
The frame header itself is 32 bits (4 bytes) length. The first twelve
bits (or first eleven bits in the case of the MPEG 2.5 extension) of a
frame header are always set to 1 and are called "frame sync". Frames
may also feature an optional CRC checksum. It is 16 bits long and, if
it exists, immediately follows the frame header. After the CRC comes
the audio data. By re-calculating the CRC and comparing its value to
the sored one, you can check if the frame has been altered during
transmission of the bitstream.