Please correct me if i'm wrong in my understanding.
This growling sound is happening because of lugging i.e we are at lower rpms but the system is asking for an upshift in gears as apparently that's how Toyota got the fuel efficiency with this v4 'hybrid' motor. Assuming that previous point is correct, I would think driving in ECO Mode the whole time should be better right since in ECO mode, it stays in the current gear longer therefore the system isn't looking to upshift
ECO mode will most likely see the engine "lugging" more than it would in Normal or Sport mode. The TRD exhaust will have some drone at certain RPMs and load conditions. Try the other modes to see if that impacts anything, and if you can pin the offending noise you speak of down to the exhaust, consider swapping to the OEM non-TRD version. There may be a take-off factory exhaust available if you have someone nearby who has upgraded theirs to TRD or aftermarket.
It could also be that the Land Cruiser's quirks are not going to be what you are after in the big picture, and if that is the case trade-in value should be decent if you really need to be driving something else.
V4 engine - Wikipedia
^^ just so you don't become laughed at, your Land Cruiser's engine (as mentioned) is an inline 4