The only fan that absolutely, positively needs to be connected to a fan header on the motherboard is the cpu heatsink fan. The pc will not operate if the cpu heatsink fan is not connected to the cpu fan header
The cpu heatsink fan is usually (but not always) the only fan that can be monitored and speed adjusted by the system. There's quite a bit of variation even by the same manufacturer. My motherboard has 3 fan headers but only monitors and controls 2 fans.
Connecting two fans to one fan header on a motherboard is not recommended.
The easiest thing to do is to simply connect the extra case fans to the power supply. Otherwise, if you really want to control the speed of the extra fans, then you will have to get a fan controller.
I have the Lancool Dragon Lord PC-K60W with the narrow side window. Ventilation, airflow, and cooling are excellent. However, I added a second fan to the front panel to balance the airflow and create a wind tunnel effect:
Your Option 3 is the best in my opinion. And I agree that you must snip some yellow wires. When you connect two or more fans in parallel off one mobo fan pinout, you DO need the black lines together (Ground) and red lines together (varying + VDC), but NOT the yellow lines. Those lines bring a pulse chain back to the mobo from the fan motor. Running more than one pulse chain from different fans at slightly different speeds into the mobo speed measuring circuit is bound to confuse it! So connect to the mobo only ONE yellow line per port, and live with being unable to measure the speeds of any fan whose yellow lead is not connected. I do NOT understand why adapters are sold that connect the yellow leads in parallel, too!
In earlier posts I have read people's opinion that most fan pinouts on mobos can handle TWO normal 3-pin fans, but maybe not more. The limit is not the steady-state operation (e.g., 3W fans in parallel on a port with 12W capacity). The limit is in the START-UP current necessary to start TWO or more fans simultaneously. It is common that start-up current may be twice the running current.
By the way, the Antec TriCool fans mentioned in one post are an interesting example of one route. They are intended to plug into a PSU output that is always 12 VDC. But they also have permanently attached a little 3-position switch on the end of a short cord. The idea is that you manually set each fan to Low, Med or Hi speed with its switch and leave it that way. So you can set speeds other than full speed for each such fan individually, but it's not something you would change often because you have to open the case for access to the little switch.