Possible good news from TrickFlow
All this stuff is automated, either someone messed up mounting the part or something changed with where they zero from on the casting.
I've got a couple decades experience with castings and forgings - no two are identical. Processes can only be so precise. The number of variables involved is mind boggling and can be affected by anything from how hungover the operator is to what the weather is on any given day.
In sand casting, parts the size of a manifold are likely more than +-.100 from end-to-end. That means the zeroing also has to shift as the part does. Which feature has to be better located to the casting: the thermostat bolt pattern, or the ports, or the carb flange? Often, there's no good way to get all three unless you whip out the part stretcher/shrinker (if only..). In fact, I'm dealing with this exact situation on some extrusion at the moment, all due to normal process variation - and my part is nowhere near the size of a manifold.
There are processes which can hold better tolerances, but the tooling costs alone can quickly exceed million$ for parts that size. Which is fine if you're making a crap load of them, but the volume for our parts is probably insignificant in the casting industry and so we get sand castings.
Automation doesn't make things simple, it really only helps improve throughput, and the final dimensions are more of a function of the casting than the machining. It's also not uncommon for castings to vary through a run, and what might have started well-aligned drifts. Or an operator can mistakenly make too large of an adjustment or adjust for one casting and forget to undo it for the next. QC should check it, but go/no-go gauges can also sometimes miss things since they have to account for all kinds of variations in geometry. At the end of the day, if someone gets a lemon the solution is calling the vendor and informing them. Companies only respond to what costs them money. If no one complains about ugly holes and bad surface finish then the assumption is that the market will tolerate it.