FIA GT is restricted only in that the cars are homologated to a blanket ruleset that disallows many of the modifications to a street car that Super GT allows.
For instance, by FIA GT standards the Toyota Supra hasn't had a legitimate engine package since the mid-90's. Using the SW20 generation MR2 four cylinder at first, and then later switching to a turbo variant of the Lexus LS400 V8, were both Toyota JGTC/Super GT solutions to the problem of the Supra's big six - poor weight distribution for road racing.
While the JGTC/Super GT series welcomed the engine swap, along with a host of one-off suspension bits, much wider tires, custom one-off bodywork, and sequential gearbox installed in the Supra, the FIA GT would have none of it as it has nothing to do with a manufacturer produced Supra.
On top of that, by the time of the V8 swap, there was no production Toyota Supra, another thing the FIA GT frowns upon.
In the case of the Maseratis, they were hamstrung in the beginning of their entry into FIA GT. A narrower rear wing, diffuser regulations, and air inlet restrictors all combined to slow down cars that the FIA (and ACO) believed would steamroll the existing GT1 grid.
In FIA competition, the restricted Maseratis still proved formidable, but were right in line with GT1 spec Ferrari Maranello GTC's, Lamborghini Murcielago GTR's, Saleen S7R's, Corvette C5R's, and on down the line.
The cars were taken to Super GT because it was thought that the looser rules of Super GT would allow the Masers to run in unrestricted spec, thus giving them the edge they'd always wanted to show AND finally giving Maserati the success needed to justify the huge expenditure of the project.
Unfortunately, the Maserati MC12 was still woefully restricted in Super GT and was unable to find a competitive edge on the existing Super GT teams (non-factory Maser vs. factory supported Japanese teams) especially with a car intended to have 670+ hp, taken down to less than 500.
It's no small wonder that FIA teams, even with the supposed "rules parity" that Super GT is bragging about in their new sanctioning alliance, have little to no interest in Super GT. Unless Super GT applies FIA GT rules across the boards and thrusts the silhouette specials from Nissan, Toyota, and Honda into obsolescence, the series will continue to be a Japanese regional series in the same vein as Belcar and Trans-Am.