Your questions don't make sense because there's no initialisation in Perl in the sense that you're picturing. Here's what you are missing:

• "=" doesn't denote an initialiser in Perl. It's always just a normal assignment.
• BEGIN blocks are executed as soon as they are compiled.
• use Module; is the same as BEGIN { require Module; import Module; }.
• Using require to load a file simply runs it as any other script (if it's not already loaded). It is both compiled and executed.

Taking a simplified version of your code

#main.pl
use Gbl;
BEGIN{
  $Gbl::runContext = $Gbl::runSMTP;
}  
...
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# GBL.pm
package Gbl;
our $runSMTP = 2
1;
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Let's apply what I've said above to determine the order in which everything is executed

main.pl

Compile the code. use Gbl; is compiled. use Glb; is executed. (BEGIN blocks are executed as soon as they are compiled.) require Gbl; is executed. Gbl.pm Compile the code. package Gbl; is compiled. our $runSMTP = 2; is compiled. 1; is compiled. Execute the code. our $runSMTP = 2; is executed. (This is where 2 is assigned to $runSMTP.) 1; is executed. import Gbl; is executed. BEGIN { ... } is compiled. $Gbl::runContext = $Gbl::runSMTP; is compiled. BEGIN { ... } is executed. (BEGIN blocks are executed as soon as they are compiled.) $Gbl::runContext = $Gbl::runSMTP; is executed. (This is where 2 is assigned to $runContext.) The rest of the program ("...") is compiled. Execute the code. The rest of the program ("...") is executed.