Airflow is important. But you don't need gale winds inside either. Just a good, steady constant flow. One of the better advantages of AIO's is that cpu temp as such from an aircooler is largely removed as a factor. Even as an intake, you'll only see case temps go up by an average of 2°C or so. The vast majority of heat inside a case will be due to the gpu. And 1060's at a max 120w are not exactly hot running to start with. As long as you have some air intake, a single 120mm exhaust at rear is fine. A 240mm AIO like the Evga 240 CLC will provide plenty of air intake. Cfm is cfm, the air is not restricted as much as it would seem. Higher sp fans on radiators still put adequate air through the rad. The restriction is more in the form of that air not reaching further back into the case, not the amount of air input. With a smaller case, that's not so important as the draw from the exhaust will create a lower pressure area by the fan, and nature abhors a vacuum, so any air from the intakes will naturally gravitate towards the back of the case, taking gpu heat with it.
Putting an intake on the side would be a mistake. That air intake would blow directly onto the gpu/mobo, and while artificially cooling them according to sensors, will also push heat back towards the AIO's intake, which over longer periods of use ends up as a hot spot, right at where most drives sit. If anything, that side fan should be used as exhaust, with a low rpm fan to pick up gpu heat and exhaust it out before it rises, a high rpm fan doing the lions share of the work would leave the top front as the Hotspot.
You want natural thermal vectors to work for you, not against.
For htpc's cpu temps are not nearly as important a number as benchmarks would have you believe. It's of far more importance to have as silent a pc as possible. The cpu does not care if it's 45°C or 60°C so having a smaller cooler that's screaming away to get you 45° is a whole lot less useful than a larger capacity cooler with inaudible fans churning out 60°C under any workload. As long as the cpu remains under @ 70°C, actual temp is a useless number. For htpc's use the biggest capacity cooler you can cram into the case, it simply means the fans can be turned down in rpm until near silent, even if the cpu temp goes up a little. Higher cfm silent exhaust fans are also a bonus.
Nobody wants to watch a movie with a htpc that sounds like you are driving 60mph with the window down.