Dimming LED using Transistor as a Switch or as an Amplifier?
First of all, keep in mind that LEDs are basically current driven, not voltage driven. Most commercially available LED strips are voltage driven to the outside, because the simply add some dropper resistors. And here we touch the reason why the first option is often preferred: 

Efficiency. Not taking power needed for the controls into account, if you run your LEDs with a PWM duty cycle of 50%, then they will also consume 50% power.

If you limit the current on the LEDs by adding a resistor (or a transistor that is filling in the role of a variable resistor here) then you can limit LEDs to 50% power, but you also waste a lot of power in that resistor.

Regarding the flicker, there are many people that claim many things about what they can see, but no one can see a couple of hundred Hz (google persistence of vision for more information). You might run into the issue of it being audible then though, so you might want to up it into some non audible range of quite some kHz.

As a further option you might want to add some buck regulator that is current driven; that way you lose only some power in the equalization resistors for parallel LED strips, but have a rather efficient reduction of power delivered to the LEDs.