There is no specific "rule". Every opening is different.
After 1.e4 c5 2.Nf3 d6 3.Bb5, 3...Bd7 is simply safest. It forces White to react to the threatened Bishop. Interposing with the Knight is a line, though far riskier as it gives White time, you self-impede the development of your Bishop, etc.
Same reasoning for White in the Bogo-Indian.
1.e4 e6 2.d4 d5 3.Nd2 c5 4.Bb5+ (First off, too soon! White should play 4.exd5 or 4.Ngf3. However, besides that, is it not obvious that Black would be more than happy to trade off his Bad Bishop for White's good one?
There are no hard and fast rules in chess. All rules have exceptions. For example, White King on the 6th, White Pawn on the 5th, Black King on the 8th, all on the same file, is a Win for White no matter who is to move - WITH ONE EXCEPTION!! If it's a Rook Pawn (i.e. WKa6, WPa5, BKa8 or WKh6, WPh5, BKh8), it's a DRAW!
You need to look at what each legal move does for you, and in some cases, which is the least evil. Interposing a Bishop with a Bishop threatens to trade (or win the checking Bishop if it's unprotected). Blocking with a Knight not only pins the Knight, but impedes the development of your other pieces in some cases. You must watch out for this. But again, there is no hard and fast rule that applies 100% of the time!
I noticed in several chess openings that the preferred book line for blocking a bishop's check is to interpose with another bishop, rather than to interpose with one of the knights. Is this merely to avoid a "self-pin"? Or is there another idea behind it, like maybe "putting the question to the bishop" in a different way?
I'm also curious about the nature of such checking attacks. I've read that the Bogo-Indian Defense tends to be drawish because of this exchange, but does that mean that all such bishop-checking attacks tend to be drawish?
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(p. 221)
Self-Pin In problem composition, voluntarily moving a piece into
an absolute pin. In ordinary play, it's usually an error--blocking a
check by putting your own piece in a pin instead of simply moving
the king off the line.
Pandolfini, Bruce. 1995. Chess Thinking. New York: Simon & Schuster.