On our portal site, our Toyota inventory is showing in stock when it's still in-transit.
Are you inputting your in-transit to early into your DMS and they are being pulled in HomeNet from the DMS?
Most OEM feeds, Toyota included, can come from the OEM - but the second your website provider sees the vehicle in the syndication feed from provider they remove the "in-transit" vehicle from the OEM and use the syndication data == it "overrides" the OEM feed.