The Gra (ח"מ סי' פ"ז ס"ק מ"ו and in much more detail in the שנות אליהו ליקוטים at the end of זרעים) offers a completely different pshat in the sugya of ההוא רעיא.
The Gra is bothered by a number of questions:
1. The Gemara says לסוף אמר להד"ם, what is the לשון of לסוף? What is this at the end of? This is the רועה claim in Beis Din.
2. Why doesn't the Gemara ask right away from the din of שבועת היסת? As soon as ר' זירא said that if we hold like ר' חייא the רועה would be חייב a שבועה the gemara should have asked even without ר חייא the רועה is חייב a שבועת היסת? Why does the Gemara wait until after we are מהפך the שבועה, it makes more sense earlier?
3. The Gemara asks at the end, ותיפוק ליה דהוי רועה? Rashi explains that this is a question on אביי, that even if he is not a גזלן he is still פסול because he is a רועה, so why did אביי ask from גזלן? However this is very difficult as גזלן is more חמור then רועה (it may be דאורייתא while רועה is for sure only דרבנן).
Based on this the Gra adopts the גירסא of the רי"ד that changes the placement of the word לסוף. Their גירסא is אמר להד"ם ולסוף אתו סהדי. The pshat in the gemara is as follows.
The רועה and the owner come into Beis Din. The owner says I gave you 5 sheep and the רועה says להד"ם. The רועה then takes a שבועת היסת like every כופר הכל. Then לסוף, after he has already taken a שבועת היסת , then 2 עדים come and say that we saw him give you 2 sheep. This answers question 1. The לשון of לסוף makes perfect sense, it means at the end after he already took a שבועת היסת the עדים came. ר' זירא then says, if we hold like ר' חייא the רועה would be חייב a שבועה דאורייתא and even though he took a שבועת היסת he would need to take the שבועה דאורייתא because it is more חמור. This answers question 2. Now we understand why we can't ask from שבועת היסת, he already took one. It is only after אביי says that he is a גזלן and therefore the owner swears that we can ask from שבועת היסת. The question is, since he is a גזלן the original שבועת היסת that the רועה took is null and void so let the owner swear and collect. To that the Gemara answers תקנתא לתקנתא. The Gemaras last question is not on אביי, but rather how could we have given the רועה the original שבועת היסת, he should have been פסול. This answers question 3.
The Gra points out that with this pshat we understand where the שו"ע got the din that is mentioned in סי' פ"ז סע' י"ד from. The שו"ע writes that if a person is כופר בכל and takes a שבועת היסת and then an עד א comes and is מחייב a שבועה דאורייתא he has to take the שבועה דאורייתא. The Rama then comments that if he takes a שבועה and it turns out that he was פסול the שבועה is null and void and he must pay. The באר הגולה and others cannot find a source in Shas for these. The Gra says that based on his pshat both of these dinim are explicit in our Gemara.