My policy is to don't care just plug in and play..
:mrgreen:
Yup .thats the way to do it...
Btw have a look at this little buffer scenario ....
The above is a typical boss buffer with colored arrows pointing directions of signal.
Blue > guitar input
Green > effect
Purple > dry out
Now lets assume the Cin is of a typical 0.047uf and the Cout 10uf.
Since your clean has to go through the buffer (BJT) before being split, your clean tone is effected by Cin which pretty much cuts bass (i will refrain from talking about treble loss/add here).
But if you were to mod it to a bigger value the effect gets too much bass (you loose your tight pants:mrgreen
So pretty much what you do , your clean is goin to be affected by either Rin, Cin , 1/2V R and the BJT which may not be 'the correct' devices for a proper buffer.
It gets worst when you true bypass a buffered effect and leave the buffer intact on the effect part ..most time you can get away clean but volume mismatch lurks to surprise the uninformed.
So is the buffer good or bad?
It has it's purpose and understanding them will assist you getting you what you want/need.
Beside "taming" impedance making a high impedance input(guitar) into a low impedance output, buffers also keeps out any bleed through from "within the effect".
Without a buffer, each time you introduce another pedal or a cable, more noise gets into your system since guitar pickups are high impedance devices that are particularly susceptible to noise from power transformers, LCD screens, power cables and stage lighting. But if you introduce more buffered devices, stack em in a chain you will have tone degration and noise too. Read article below.
You can design or mod an existing buffer and enhance it's performance to suit (thats what was done to that "on sale" boss you just mentioned) and have it 'inline' with bypass signal to avoid mismatch.
Common Buffer types
opamp >> almost a perfect buffer.. in a scope the input and output will match exactly.
transistor >> less parts and some say it's a more musical sound but it is not a perfect buffer.

(just like you and me)
On the other end you have a Fuzz Face type which is a mother of low impedance devices(thats why the FF was one of the first true bypass pedal). Having a buffer (low impedance) before it just makes it go crap ... so here we need a
switcher or a pick-up
simulator to get the impedance right where the low output is bummed back up to drive a low input impedance device. This only applies if you are using an active(low output impedance) guitar or bass.
In conclusion , understand impedance ...
for some read
http://www.muzique.com/lab/truebypass.htm
must read
http://www.stinkfoot.se/andreas/diy/articles/bypass2.htm
more
http://www.whirlwindusa.com/tech03.html