To clarify, the Thunderbolt/USB4 host controller and PHY are integrated into the M1/M2 SoC and are based on
Synopsys DesignWare IP. The
Intel JHL8040R is just a Thunderbolt 4 retimer chip. The M2 version of the 13-inch MacBook Pro also uses the new U09PY3 retimer. iFixit missed that, but
competitive analysis firm TechanaLye noticed it and has already opened the chip and reported on their findings.
Nobody has publicly reported whether the U09PY3 is a semi-custom offering from a third party supplier, or if it was developed in-house by Apple. The latter strikes me as unlikely, because it's an odd component to dedicate resources to when third-party solutions are already available from long-time Apple supplier
Parade and recent startup
Kandou.