From #bitcoin-core-dev on Freenode (shesek is me, sipa is Pieter Wuille [0], one of the most veteran bitcoin core devs)
<shesek> does bitcoin core ever verify merkle inclusion proofs? (I assume not, it only verifies that the merkle root matches the set of txids. but maybe I'm missing some other ways its being used?)
<sipa> i don't think anything verifies them
<sipa> shesek: they don't even ever receive any
<sipa> though they were an essential part of BIP37 [related to light SPV clients]
<phantomcircuit> shesek, for a full node theres no real difference between receiving a merkle tree and a hash of a list
<sipa> yeah, for a full-blocks-only bitcoin like protocol, the "merkle root" stored in the block header could just be a flat hash of all txids
<shesek> does bitcoin core ever verify merkle inclusion proofs? (I assume not, it only verifies that the merkle root matches the set of txids. but maybe I'm missing some other ways its being used?)
<sipa> i don't think anything verifies them
<sipa> shesek: they don't even ever receive any
<sipa> though they were an essential part of BIP37 [related to light SPV clients]
<phantomcircuit> shesek, for a full node theres no real difference between receiving a merkle tree and a hash of a list
<sipa> yeah, for a full-blocks-only bitcoin like protocol, the "merkle root" stored in the block header could just be a flat hash of all txids
[0] http://pieterwuillefacts.com/