Transcodable codecs allow you to convert between different codecs, for example on different call legs or when recording etc. Most codecs are this type.
Some codecs though are patented and need to be licensed to use, eg G729/G723.1/AMR. To at least have some support for these they're implemented as passthrough codecs - you can pass the raw data from phone to another on a bridge without needing a codec because you're not doing the encoding/decoding. However this means you have a limitation that you cannot use these codecs for anything that needs that ability - voicemail/conference/record/eavesdrop etc, and bridging with different codecs on each leg.
If you want to use G729 that's one case where there is both a passthrough and commercial transcoding codec. mod_g729 is the passthrough one. mod_com_g729 is transcodable, but requires purchasing licenses from
www.freeswitch.org.
-Steve