Eric same thing happened to me, I went in wanting a hatchback 1.4t LT manual, didn't really care about color and the only option I was thinking about was the connectivity package, the dealer only had one turbo in a sedan ltz..
of course they kept puushing me on that or a 1.8 hatch. And after looking for about 3 days they found a car that matched my criteria. And it was 100mi away so they had to do a dealer trade to get it. But now I'm the proud owner of an inferno orange LT hatch 1.4t 6MT. But the turbo was really rare at that time (may 2012)
I recall either reading on here or maybe from the salesman that when they started production they stated with the 1.8 and made xx cars in a certain color and certain trim and would then produce xx cars in another color and so on and so forth with different packages and engines being put into production after the previous batch was done..
What I got out of it was that not all engine,color,trim levels were available at one time they were phased into production after a particular package was run. And apparently gm held out on the turbo engine for awhile and the turbo manual much longer
-tyler