No difference between the features, only how you use it. Pixels connected to an ad account are available ONLY to that account. Pixel created via FBM can be shared between all the ad accounts and users of the FBM.
Never had the need to create so many in one go, but yeah, pretty much. If your websites are all legal, and you’re running sufficiently regular campaigns, you can actually just reach out to customer support and they will be willing to increase the number of pixels that can be created, I’m sure.