Hello Mahmoud,
Actually I been away from the community for the last couple of months due to my engagement in multiple projects, this morning I been able to catch up what I missed and found your article.
I worked deeply in inventory reconciliations to GL with many customers and noticed many issues that cause variances, but never seen the case you just mentioned, and therefore I tried this over my test box and can confirm that I got the same result, I have tested this over all my GP versions (GP 10.0, 2010 and 2013) with same results returned.
I guess this is a bug that need to be reported as I cannot see any business justification behind this and would advise you to initiate an incident request with Microsoft to let them know about this case and the business impact behind this, the good thing is I been able to locate this difference in the Reconcile to GL utility created for Inventory in GP 2013, the transaction has shown as matched but the amount is different:
I will be using Microsoft Connect to report this and hopefully they can look at this one day!