The world of coffee is one of great diversity. Different shops' standards may well generate a coffee that is of a different style than is currently popular, but that doesn't necessarily have to mean inferior. The key is to understand what your product is supposed to be when it's at its best.
The SCAA is a fantastic organization and their training material and methods are great... however it pays to remember what their definition represents. It is a guideline to help understand American espresso and one way to achieve it. It is not meant to be the last word. Looking at "the SCAA way" as right and your company's way as wrong is not terribly helpful.
I do quite a bit of service work for large national chains, and found the aspect you're describing to be a big challenge at first. What I found after a while though was that there were bars within these systems that were achieving coffees that were far better than some of their sister stores. There is still a benefit to doing things well, even if that benefit is only that the product isn't nearly as bad as usual.
That said, if your large coffee company has been around for a while, chances are good that there is a zone within corporate standard practices that your products will be decent. Explore the range of shot times, espresso doses, shot volumes, and find the small zone within those ranges that gives you best results. Focus on cleaning - chances are good that there's no prohibition on keeping your stuff spotless. Train for consistency. Push the boundaries just a bit where you can if an improvement is to be had. If you can, visit the stores in your system that are supposed to be the best and see what they're doing.
Train your baristas to be the best possible in all the ways you can control. Chances are good that, even with tight rules, you can still get them 90% of the way there.
In short, make your product the best it can be. If you find that you really can't stand behind your company's product at its best, you have a bigger problem... but in the meantime, a good working goal might be to make your shop serve the best cup of Staribou in your market.