They do, actually!
Most car manufacturers, including Toyota, now use the MOST-bus for infotainment system interconnects, which is an open standard. So your car being a >2010 Toyota, it will have a MOST system.
> I can't justify replacing the system in my 2016 Highlander just to get Android auto
You don't have to, there are plenty of aftermarket modules available that will add Android Auto to your existing MOST infotainment system. Can be a hit-or-miss though in terms of quality and integration. If you want something reliable and well integrated, stick with the OEM solutions.
> I don't like having to rely on the manufacturer nor Google/Apple for connectivity basics.
You're already relying on the car OEM for mobility and your safety, and you're already relying on Google or Apply for connectivity (aka: your phone's OS).
Remember that your 2016 Highlander (3rd gen XU50) was introduced in 2013, so developed well before that. Android auto didn't even exist back then, and we still hadn't consolidated on the iOS/Android duopoly we have today. Heck we were still using Windows phone and Blackberry OS back then. How could Toyota engineers have designed something that would still remain compatible with devices in 2025? Quite remarkable actually that it still works at all.