Detective time: Now that we know
for sure that it's set around the centre of Kyoto Prefecture, we can figure out exactly where the manga is happening.
'Azeno-cho' as it is called in universe is in reality
Kyotamba-cho.
Shunpei's middle school is
this place.
This angle looks close enough to what's shown in the panel.
The main bus stop is
Hinokiyama bus stop; it looks exactly like it does in the manga and is a ten minute walk away from the school.
It seems to be the main stop of the area so like ten buses branch out from it - the exact bus Shunpei and An take is apparently
Shitsumi line.
The Hachiman shrine in
Chapter 12 is the giveaway, again the entrance
looks exactly like it does in the manga.
Shunpei and An's places would be a bus stop or two up and down the shrine.
An's stop is probably
here, doesn't match exactly but does seem pretty accurate. Not entirely sure where Shunpei's stop would be for now.