I use Inline::C for some production code, and had to work around the issues you described. My solution was to create some infrastructure for precompiling the XS generated by Inline::C when requested. So when developing, I run using Inline::C, and get automatic recompiles when I change the C code. To release, I run make precompiled, which is a target I defined to force compilation of all of the Inline::C code and copy it over to the installation location. At runtime, the module chooses based on an environment variable whether to use Inline::C or the prebuilt stuff (on a production machine, you don't need to install the Inline module at all.)

In more detail:

Each of my Inline-using scripts looks like:

package Whatever;
BEGIN {
  do ($ENV{DEVEL_MODE} ? 'MyMagicInline' : 'MyMagicDirect') or die $@
}
...perl code...
__DATA__
__CPP__
...C++ code... (ok I lied; I'm using Inline::CPP, not Inline::C)
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$ENV{DEVEL_MODE} is set automagically by something else, but don't worry about that. Just always have it set while you're developing.

MyMagicInline contains something like:

use Inline with => 'MyScriptInline';
BEGIN {
  $inline_code_file = abs_path($INC{__PACKAGE__ . ".pm"});
}

sub find_code {
  local $_ = shift;
  s/^.*?__CPP__\n//s;
  return $_;
}
use Inline(CPP => $inline_code_file, FILTERS => \&find_code);
Inline->init;
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The MyScriptInline file contains a single subroutine named Inline that returns a hash ref of Inline settings (eg { INC => '-I/my/path' }). (This is how Inline implements its with magic.)

RxMagicDirect contains only

require DynaLoader;
{
        my ($pkg) = caller(0);
        push @{$pkg . "::ISA"}, "DynaLoader";
        bootstrap $pkg;
}
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Ok, so that's just a sketch of what's going on; there are details about where the files are found and the precompilation target that runs everything under Inline and then copies the generated *.so files to the appropriate lib/ directory, but the end result is that I can install onto a production machine and not have to install Inline there.

I'm sure this isn't the cleanest way to do this. I never really bothered to go back and clean it up after I got it to work, but it seems to work quite well for what I need.