The difference is mainly with EE cyclerate the "effective" EE clock is being reduced, is like saying the PS2 processor was slower and then easier on the emulating machine. And this might indeed cause some issues in some games mainly when abused. But... (always there is a but)
Those other hacks like halving the base frame rate destroy almost every synchronization out there, where with EE cyclerate the "EE" being emulated had relative control of syncs, now it has none, but (again but) this might work in some cases but becomes very sensitive and needing adjusts at each different game being played, critical and not trivial adjusts. And this is the reason it is not directly implemented and not recommended in general fashion at all. Just to give idea, the turbo already helps creating more issues, so is being used at least two uncontrolled issues sources at least.
In despair cases such drastic measures can be attempted, the user just must be aware of potential problems and know what is being done.
The main problem arises from the misunderstanding of what is that base FPS on the emulator in relation with the actual PS2. In the last it is the Refresh rate of the TV standard being used, it is so critical that is hardware controlled. It is the same as the refresh rate on your monitor/video card couple. If it failed on actual PS2 the consequences would be... dramatic to say the least.
But since to the emulator it is only an "emulation" of that refresh rate that most games use to sync their events, the effects are less dramatic but still extremely unpleasant.
So, it's true that in actual PS2 some games run at smaller FPS than that "fixed and critical refresh rate"... they are different things indeed... but make no mistake, does not matter PS2 FPS, it's output will be steady 60 or 50 lines per second.
I hope this shed some light on that so little comprehended "base FPS" and how it is confused with how the motions on the screen are felt, the poor thing is even called fake when it is honest
(a little explanation here is in order... what really becomes distorted is the pace the action happens; like a movie in slow motion despite the frame rate is the correct).