I've heard there can be issues with clicking noises when using PWM fans so that leads me to option 3, using the R4's fan control. I'm just not sure though. Any advice would be appreciated.
While clicking can happen, it can happen with all fans, i have had TY140 that click others dont at the same rpms and pwm, its hard to generalize. I can tell you that all 7x NF-A14 PWM that i bought and a NF-A15 PWM none i have percieved any clicking, if there is, i cant hear it, but this is not a guarantee that none will. PWM fans are not better or worst than 3pin fans, i personally prefer them as when i moved on from ASUS was with the mind of not depending on software to control them, so MSI bios works pretty good with them, but if i were on ASUS i would probably wouldnt have chosen PWM fans for all spots (just the cpu).
What I would really like to do is have the fans at auto so that as temps heat up inside the case, the fans adjust themselves. Is that possible through any of the 3 options?
No option 3 the only one that will vary is the CPU fan, the others will be binded to the fan controller on the case meaning they will run steady at certain rpms no matter the cpu temperature. So chose either option 1 or 2, depending on what you are aiming.
It seems like options 2 and 3 both control the fans as a group, one just uses PWM and one uses voltage, is that correct? Is one preferable to the other?
Only option 1 can be controlled individually (all dependant on the CPU temp on the ramping, but you can define for each fan), option 2 all are dynamically controlled, but all binded to the same signal, so if the fans are the same will be the same rpms (varying depending the CPU temp), option 3 is only the cpu fan controllable and the rest are on the 3pin fan contoller on the case.
My suggestion, as you already went with Asus motherboard, is to go with 3pin fans for the case fans, and only use 4pin PWM fan on the CPU, connect the case fans to headers CHA_FAN 1,2,3, and connect the cpu fan to CPU_FAN, and run AI SUITE / FanXpert, run the tuning and check the graphs for each fan, if they are to your liking in terms of noise and temperature, else change them. Now if all this fail and you cant or dont like what you are seeing, its simple, just connect all the case fans to the Define R4 Fan controller, and just use the 3 setup switch to see what you want. I would only recommend PWM fans if you were going into another brand of motherboard or if you were using all your fans the same, but for practical purposes, i think its better in your case to go with 3pin fans, more options to play with and no restrictions.
I do recommend you read the SPCR reviews that i linked you in my above post, the best sound fan was the Antec True Quiet 140, and if you want a little more cooling the Phantek 140 and Antec TwoCool 140 are also good options, all better than Noctua according to the SPCR reviews. But i also recommend you before buying fans, test the Fractal fans in both the CHA_FAN 1,2,3 FAN headers and on the Fan Controller, and play with it and see if you really want to invest on quieter fans. And if after playing with the included fans, you feel you need something better, consider antec true quiet 140
seems like good option out the SPCR review, and specially as they are very cheap compare to Noctua or Noiseblocker, im about to buy 3 for my server.