I worked in the industry for several years and my opinion is that boat manufacturers are just like car makers. All cars have to pass safety test and so do boats. Tracker, Lowe, G3, etc are the Ford and Chevy of the industry.
I would look at the features and not get too hung up on any popular brand because they all hold up well and retail tends to be prorated among them.
There is one minor difference that might matter to you regarding a pontoon, Lowe puts foam in there pontoons and Tracker doesn't as far as I know. At least the didn't when I was involved.