That is correct. To me it seems unjust to force the weakest weapon in the game to carry such a gargantuan downside. With a sword, you can add damage with a high strength score, trip someone, make attacks of opportunity, etc. With a bow? Nope. You can make attacks at range, and that's it.
If you must, think of it this way. A human's profile is perhaps two and a half feet wide for a rather large person. I myself have a widest dimension of slightly over 15 inches at the shoulder. That's about a quarter of the width of a tile. We'll go into a diagram again, this time subdividing the tiles into 16 parts.
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# # # #
# # # #
# # # #
# # # #
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■ ■
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Archer: ■ (A wide-ish human.)
Ally: ☻(For this example, I'm using extremes. This person is thin and holding fairly still. Hell, let's make them a halfling so they're short, too.)
Enemy: # (In this case a gelatinous cube because they take up a whole tile and that's convenient.)
The archer, so long as they aim at the cube at all, has no line of fire towards their ally. Due to the current rules, the cube already gets cover from the ally anyway for +4 AC. (Not that that will really help this 6 AC monster, but that's besides the point.) That archer's optimal line is straight north. To shoot that friend, they would have to veer off to the right about 25 degrees. That's not 'messing up', that takes some serious effort. This is an extreme example, of course, but it shows that just because someone is in a nearby tile doesn't mean that they're in danger of being shot. In fact, we can explain the need for the Precise Shot feat this way.
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☻ ☻
☻ ☻
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In this example, the burly human paladin is stabbing that gelatinous cube right in the flat gelatinous face surface. The archer still has a shot, of course, but now their aim might only need to be off by 5 degrees or so to hit their ally. Of course, a smart archer would try to aim to the left side of the cube because of that... increasing their chance of missing to the left. They're not going to fire straight on and possibly hit their friend. Thus the shot takes a -4 penalty. An archer with Precise Shot is confident enough in hitting the mark that they'll just fire right at the gap and avoid that -4 penalty. Note that their ally being in the way also gives the cube cover.
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Now the cube has no cover, but as the arrow could still veer off and hit the paladin, there is still the -4 for precise shot.
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An interesting quirk of the rules: With the paladin behind the cube, the cube gains no cover. For some strange reason, the archer still takes the -4 from precise shot. (Normally it could be attributed to the arrow going past the creature and hitting the ally, but cubes take up a whole space. Maybe the archer's afraid of piercing through the cube right there because it's so soft. I dunno.) If the archer completely botches this attack and misses the gelatinous cube - which I must remind you is almost impossible to do without a natural 1 because cube AC sucks - you roll a 1d8 to find out where the arrow lands. Whoops-a-daisy, rolling a 2 means that you arced that arrow over the son of a bitch (or just past the creature if it's not a cube) and stuck your ally for full damage. BUT WAIT - the cube is in the way. Your ally gains +4 AC from cover from a standard monster, but because the cube explicitly blocks line of effect, the arrow can't reach him. The arrow simply disappears from reality without hurting anyone, as it hit neither its intended target nor its intended resting place.
That said, against a standard creature on a natural 1, you automatically miss the enemy. If an ally's too close, they might be hit. That's already bad enough.