You should strongly consider hiking in trail-running shoes, especially if you are thru-hiking and walking loooong days:
a) Trail-runners are lightweight and hence much less tiring for your feet and legs (some say 100 gram on your feet equals 500 grams on your back, as your feet are in constant motion and need to be re-accelerated for each step; I think they are referring to some physical laws of “inertia” here). Lightweight shoes is an important safety consideration as tired legs are more prone to injuries as you loose feet-concentration and risk a “misstep” where you’ll roll your angle or possibly even sprain or break it. Exhausted legs are an accident waiting to happen and heavy boots will catalyze that.
b) Trail-runners are soft and flexible and you avoid the prolonged blistering period of “breaking them in”. Granted, hiking boots do last more miles once they are broken in, but the net-effect is still clear: you’ll spend less time breaking in your footwear, if you hike in trail-runners.
c) The “rule” says that you’re only supposed to wear hiking-boots if a) you have an off-centered angle-structure and hence need extra angle-support (referred to as bio-mechanical feet problems, in fancy language). Or b) if you carry a heavy backpack, say base-weight above 30 lbs (14kg) which then also limits you’re daily mileage considerably and likely kills your thru-hike ambition.
c) Expect your trail-runners to last 400-700 miles and hiking boots to last 900-1200 miles. Economically, there shouldn’t be much difference as decent hiking boots also rings-in at roughly twice the price of decent trail-runners. This mileage means that you’re looking at 4 pairs of trail-running shoes for a PCT thru-hike. However, don’t be surprised when you come across the happy, broke student who push a thru-hike in 2 pair of shoes, though you can barely recognize the model and sometimes doubt that the “thing” on their feet would any longer classify as shoes.
d) You can choose to buy new shoes whenever the first holes develop (250 miles), but then you’re probably looking at 6-7 pair of shoes. Consider stitching them up with a strong needle and use dental-floss as thread (this works for any strong gear-repairs, say if branches have torn holes in your backpack or jacket).
e) In-soles? I didn’t have any and many don’t. However, everyone who uses them are thrilled, so I believe there’s something to it. They provide some resistance against sole-distortion, stabilizes your heel so it doesn’t slide and give extra arch-support. SuperFeet seems to be the preferred brand. Maybe you can avoid the common lifetime “souvenir” of a thru-hike if you choose to use in-soles: you go up 1/2 a US-size in shoes (1 EU size) as you flatten your arch during the 5 months of walkning.