Even though the Kesef Mishna and the Gra disagree about what it means יש קניין לעכו''ם להפקיע מידי תרומה ומעשר it is still hard to see if there in ant difference in terms of practice. Though I do admit the approach of the Beit Joseph helps to understand the Gemara in Rosh Hashanah page 13. Thee it asks how could Israel bring the Omer from grain that grew in the property of the Canaanites. [Though I am wondering what the Gemara means there. Did Israel bring the omer after or before they reconquered the land that the grain was grow on.?]

The basic subject is this: The Rambam says there is no acquisition to a idolater IN Israel .So If a Israeli buys the land back, the grain that grows on it will be obligated in truma. The Kesef mishna says :this is even though the Gemara seems to hold there is acquisition, still it must be (according to the Rambam) tat that is not the law. Or that the Gemara is referring to the time when the field is in the possession of the idolater. 

The the Mabit brings that the Kesef Mishna himself was aware of this problem [that even if the land is owned by the idolater, it still is obligated in truma as the Rambam himself says later in that perek.]

So the Beit Yoseph answers the grain is obligated when the smoothing was done by a Israeli. 

Well even though the Beit Yoseph seems like a very new idea--that all agree that when the land is in the possession of the idolater it is not obligated, still if a Israeli buys the grain and does the smoothing of the stack, it is obligated, so where is the argument? The Gra agrees.  The Beit Yoseph himself brings this. So in the long run, where is the argument.

I am sorry for bein short and not explaining what I mean in detail , but it is really really late and I am really tired, To see what I mean look at the the Gemara in Avoda Zara page 47 and the Avi Ezri on First Fruits perek 2, laws 10 and 13