The design of that crossover pipe is absolutely nothing with which you should be concerned to the point you start removing stock tubing in favor of round tubes.
Pipes are formed in specific shapes for good reasons - typically for either access (getting a tool to a fastener behind a pipe) or clearance. The simplest form of a pipe is round and straight - they don't deviate from that shape for sh!ts & giggles. Once the emission gasses pass through the converters, it's all about acoustics (sound) and volume (inside the tubes, collector, adaptive valves, muffler and any resonators, etc.). The volume in that area of the crossover pipe is pretty much the same as the round tube portion would be. When making pipes with these types of features and using the cheaper manufacturing methods for high volumes (quantity), material is typically moved around, not removed or reduced (or that is at least the goal) during the forming process.
There are GM requirements for clearing both vehicle undercarriage, surrounding components as well as ground clearance. That's what GM ends up with given those requirements. The previous generation (K2XX) crossover pipe was also formed in a similar fashion but has a different cross sectional shape in that general area. The design of that area of the crossover pipe takes into consideration the starting tube diameter/circumference, so putting a round tube in there will change nothing other than possibly start causing interference which can lead to undesirable noises or taking damage under certain conditions. The entire system is tested both virtually (simulated on a computer using 3D models) and physically literally years before these trucks are built. The entire exhaust system performs the way GM desires it to perform, even with that flattened tubing. If there were any deviations from expected flow behavior, there is absolutely no way GM would allow those pipes on production intent vehicles and the supplier wouldn't be too keen on spending money on tooling to produce parts that ended up being a detriment somehow (of course, that all depends on how GM desires the system functions as a whole, too).
However weird anything with the exhaust systems look, there's usually a very good reason GM didn't want that pipe to be round on either side or have a bash here or there. They don't make manufacturing a pipe more difficult, time consuming and costly just for looks or their own amusement. That costs GM money. The suppliers of the exhaust systems don't deform, flatten, bash, etc. tubing for looks or wasting machine production time either - that stuff costs money and they want it out of the plant as soon as possible in terms of processing time.
But hey, it's your time and money you're wasting and it's your truck - you do what you want with it.
Finally, I wouldn't waste my time responding to any of this if I didn't have intimate and first hand knowledge about the above, whatever that may be worth to you.