Just to clear things up a bit, the "ears" on the 88/05 are RIVETED. This is well documented and for anyone who questions this I refer you to "A Collectors Guide to the GermanGew. 88 "Commission" Rifle page 105. There is a later modification called the 88/14, which this particular rifle clearly is not, which had a different type of ear welded and shaped onto the receiver. These examples are now quite rare as it is suspected most were destroyed after WWII as part of the Treaty of Versaille. This modification was not one which was given to the Turks.
The "crazy rectangular cutout" is where the forward portion of the left side guide fits. For strength purposes of the guide, they cut it out rather than try to form it along the round surface. As the right side has no "height" to it, there is no need for a cutout of any type on the right.
Now I admit, I am one who is more apt to believe a book written by an expert who has researched these rifles over a period of years collaborating with many other knowledgeable people than one individual on the internet that messed with one so take this information as you will. It is however backed up by numerous sources on the internet for anyone who cares to believe such sources.
As for who removed them. It was not the Germans. There would be no reason for the Turks to have done so unless one of the ears was broken off and they had no means to repair it. This being the same for a post Turk owner.
The book is great by the way. Highly recommend it. Lots of information in there on how the rifles came about, all modifications done to them, the copycats, etc and at the end firing data comparing them to other similar rilfes. Tons of period photos.