Now that you explained that makes a #### ton of sense. The purpose of company CDL program and independent CDL schools are different. Companies want to make sure that you are able to operate their trucks for them. CDL schools are here for a profit.
Remember, your first year, clean, is a ticket to much higher paying second year and so on. Never rush, you have nothing to prove other than keeping a spotless record for year 2 application. Start applying at month 10/11 if under contract.
I'd say don't overthink it...You are going to get in with these companies and then leave..They are starter companies....Personally I'd probably consider which pays the highest, which treats the drivers the best, which has the best trucks, and who has the most terminals.
I went with Swift and the Swift Academy. Worked out just fine for me. Academy was 3 weeks. First week is about classroom stuff to get your permit (I had mine before I got there but still had to sit through it). Also during first week medical stuff for CDL physical and drug test. Second week was on maneuvers at their practice facility. Third week you also started driving on local roads along with maneuvers. At the end of 3 weeks, take the test. Once you have a CDL, you go out with a mentor and that's when you start actually learning how to do all this stuff and not just 'drive' a CMV.