NKM2401 could potentially improve things but alternatively it could perhaps make things worse; I'm not even sure how one would set about trying to determine which it would be other than to try it.
Manchester coding is used to keep a transmitted signal at a net DC level to keep the RF receiver happy and similar already exists within a normal IR receiver due to its ~36kHz modulation so it might not gain anything and glitches which would be ignored by an IR receiver may cause the NKM2401 to see that as a corrupt packet.