I believe their point was mostly that they were impressed with the ssi track and that gue was more confined to gue methodology rather than open to diving with people from different agencies. They currently are starting to offer XR courses from SSI and offer no GUE after fundies.
So, I don't know them, so I can see three possibilities
(1) they honestly believe what they said, but it would be wrong. Most of the agencies technical courses do not have any foundation course as a prerequisite. Usually, good instructors would evaluate your skills' level and, if you're ok, fine, you can go for the tech/cave/whatever course. Otherwise they would suggest you to do a foundational course. Guess what? If you do the GUE fundamental they will teach you these skills
therefore, you can do fundies and then go to other agencies. HOWEVER, however... I could not find any prerequisite for SSI, so double check it. Side note: GUE also allows for crossover, but it is a bit more complicated (it requires an instructor evaluator for the course you want to do, and there aren't many). This is why you may want to consider fundies (if you like it, and you want to continue this path, it's going to be easier).
(2) they are honest businessmen, but still businessmen. In other words, they believe they can give you a very high quality product, which is what you want, and they don't want to risk to lose you. So they suggest you not to do fundies, because if you do and you like it, they would lose you as a customer.
(3) they are not respectable business people. I don't believe this is the case for some reasons, so I will not even discuss this option.
Before continuing, an important note: if you do fundies, after the course... you can dive with WHOEVER you want. No restrictions at all about that, and you will also be a fantastic buddy.
Now, let's stick to your choice. Both courses have advantage and disadvantages. To be honest with you, if I were you and I liked the GUE instructor, I would do fundies without even thinking about it. The advantages are that you are sure of the product quality and you will have more options after the course (both GUE and other agencies). The disadvantages are that you can't choose some things (no sidemount, no jacket style BCD, etc.). The opposite is true for SSI. Obviously you must also consider how much you like the instructors...
But my view is biased
Ultimately it is a choice of you.
Whatever you choose, best luck!