Rearrange to avoid the pause. Also, a lot of English-as-a-second-language people have trouble with the word "generic", so avoid that:

Strings to be replaced sometimes need to be very specific to avoid undesired replacements.
This is a common problem with shorter values.

s/in a/in an/

"architecture dependent architecture," is confusing. Maybe the second one should be "location" or maybe the whole thing should be "architecture-dependent tree"?

s/which is/

"currently" implies it is going to change and it might be better to just leave that out, which would also make the comma at the end of the previous line not necessary.

Maybe just replace "It is generally not a problem":

For example, a port that installs a file whose path contains <literal>mach</literal>
could have that part of the path string replaced with the wrong values.  Consider this
<filename>Makefile</filename>:

s/Runnnig/Running/
s/will wrongly generate/wrongly generates/

s/Changing/Change/

passive to active:

s/will correctly generate/correctly generates/