I agree, I am not sure why they chose this as default. It really doesnt make sense to me. Open a random client and go to Illinois. Go to Tools/Miscellaneous/ and uncheck the box under OTHER INFO.

I agree 100%. The last thing a client needs is a notice from the government. Because guess what happens next? You get a phone call or email that wastes your time asking you why they got a notice. And then the client also wants to know if you made an error. No brainer to check the box that allows the penalty to be calculated on the return. The client rarely sees it. 

100% Truth right there @Ephesians3-14 

But if you asked your clients up front if they want you to calculate the penalty so that they will pay a few bucks extra now or skip the calculation and they may or may not receive a notice later, what are most of your clients going to choose?  I let the software calculate the penalties but there are times when a penalty is calculated on Minnesota and a little message pops up "this return can not be e-filed" and I'll change the prior year tax to delete the penalty so that I can e-file the return.  After doing that for a couple of centuries, I've never had a client call about getting a notice looking for a couple of extra bucks.  So do we do the calculation for the sake of the client or for our own benefit?