Well, couple things.
1.) Not familiar with CNT - I've been on this forum for a while and cruised a good number of parts sites but never heard of them. That being said, it looks like they've focused their product development on other platforms.
2.) If you go with a catless DP you will need to have the AP adjusted for it in order for the CEL not to appear. The O2 sensors will detect the difference (or lack of) in exhaust quality and it will raise a flag with the car's engine management system.
3.) If you want to bypass the CEL without adjusting the AP you can do so with a spark plug defouler such as this -
https://www.2j-racing.com/2jr-fiesta-st-downpipe-de-fouler.html I've used on on my supercharged 4Runner that I removed the cats on and I don't have the ability to tune it out of the EMS so I went with the defouler and it works! No CEL - it has shown up a couple times but I believe it was due to my muffler falling off and affecting the air flow... Either way, I clear it and it doesn't come back for weeks.
4.) In regards to the size, if you have a 3" exhaust then it's ideal to have it 3" the whole way as otherwise you don't see the benefits. That being said, this car doesn't need a 3" exhaust - 2.5" is just fine, even for hybrid or big turbo options. Unless you're going over 400hp, you don't NEED a 3" exhaust. So, will you have an issue bolting it up? No. I did the same thing - 3" Catless DP and 2.5" exhaust. The CNT option just assumes you're bolting up to stock exhaust.
5.) lastly - the catless DP doesn't have the mounting bracket that the stock option has. For me, this was a deal breaker - I wanted to get a DP that had this bracket so that the exhaust was not hanging off the turbo but was supported by the DP as the Ford Engineers intended. I went with the 2J Racing option for this reason (although I'm not sure they're available new anymore).
Hope that helps!