The three major differences between a managed switch and using Linux bridge interfaces are performance, port density, and features.
Most managed switches will embed some of their programmed functionality into specialized hardware. This is not true in all cases, but this specialized hardware will tend to outperform devices that are purely software based (at least for the functionality embedded in the hardware).
Second, if port density is of concern, there aren't many server systems where you can pack 12-48 ports into a 1U chassis, and of the ones I have seen they were designed to be a network device.
Finally, are the features. Managed switches will typically have features that either are not present on a Linux platform, not as easily configured, or may require additional CPU/memory resources that will further impact performance if you use them.
However, aside from the differences in the two platform choices, it sounds like you are setting up some sort of lab/test/dev environment. My primary concern would be that you should try to match your actual/production environment as closely as possible. Your Linux "switches" do not behave the same as your managed switches, so something you implement in the lab may act entirely differently when implemented on your managed switches.