I'm not saying I'm anything close to an expert on this stuff, but I am interested in it and have studied it through posts on this site, so I'm going to spill my guts here and hope somebody has more or better info.
From what I've read over the past seven months, I don't think anybody outside of DJI knows for absolutely sure how exactly the FPV thing works. There is no documentation from DJI on this that I've ever seen or heard of. My weak understanding is that it is extremely complicated, much more so then one might think. Not only do you have two antennas and two FPV transmitters in the RE, but you also have two antennas and two FPV transmitters in the Phantom (camera). And it seems there is an auto-switching going on constantly, as the logic board is constantly looking for the best signal on both the bird and the RE. This switching makes perfect sense for the Phantom, but it doesn't make much sense for the RE since both antennas are exactly the same, they are right next to each other and pointing in exactly the same direction. Nonetheless, the consensus is the switching does seem to take place in the RE. At least that is what we think. So if we assume that is true, it wouldn't matter what transmitter you want to mod in the RE. The RE will find your best signal (best antenna) and use it.
But the problem is the switching. Once it has that good antenna, and is using it, it will switch to the weak antenna for no reason other than to check and see if it's better. And it may hang onto that weak antenna for up to two seconds. If it's weaker than the first antenna, it switches back. So if you have a strong antenna, you're still hampered with a weak antenna and intermittent weakness because of the switching. Hence, it's probably best to mod both transmitters.
If that's not complicated enough, it gets much worse.
My understanding is, the video signal leaves the Phantom (camera) and is received by the RE. But before it's sent to the phone/tablet, the signal is checked for corruption. Details of the received signal are sent BACK to the Phantom/camera. If the details of the initial signal data are correct, then the Phantom/camera sends an "ok" back to the RE. Once the RE receives this "ok", it proceeds to send the data (video/telemetery) to the phone/tablet on a different frequency. You then get to see a picture, and you'll ideally see this picture 15 or 30 times per second if everything is working perfectly.
So, in summary, at least some data from the initial signal must move forth, then back, then forth again before you get to see anything. That is why the range is so limited.
So assuming all this is true, you have to think in terms of sending AND receiving for your RE. So you want to pick the best antenna to maximize signal strength in transmission, as well as its ability to receive. And this is why DJI chose patch antennas in their RE. Patch antennas send a transmission out in one direction, and also are good at receiving. It makes perfect sense.
And so, if you're going to replace your DJI patch antenna, you might be wise to replace it with another patch/panel antenna or a windsurfer. The point is, you want it to be directional and it's best if it's linear polarity to match the linear polarity of the patch antennas in the Phantom/camera.
There are other options if you're willing to mod the bird such as the FPVLR mods.
So this is how I understand it, and if somebody has more or better info, I'd love to hear from you.