It shouldn't make any difference (XR or not) because even the regular version doesn't have an immediate effect. It takes a few weeks to reach saturation levels in your system and then each subsequent dose goes towards maintaining that saturation. When you stop taking it, it takes several weeks for your system to be fully rid of it as well. Both versions are supposed to help reduce IR. The XR version, because it digests slower, is found to be easier on the stomach for some, but the medical properties should be the same.
Of course as with so many things medical, we don't understand all the details of what exactly Metformin does in the body, what molecules it interacts with and how, and all that. So it's not impossible that the XR version might have different effects on fertility than the regular, even if it doesn't have any different effect on blood sugar, but theoretically it shouldn't, anyway.
The main issue with Metformin is that it is a carb-blocker. You might recall some of those "fat-blocker" weight loss drugs? Where you are supposed to stick to a low-fat diet, but if you don't, the drug would stop your intestines from absorbing most of the fat you ate, so you'd theoretically not gain any weight from it. But whatever doesn't get absorbed by the intestines just goes straight through them, so people on fat-blockers who ate high-fat diets often had lots of bowel problems. It's a very similar thing for Metformin and carbs (it was in fact originally intended to be a weight-loss drug; its uses now as a diabetes and PCOS drug were unexpected side-effects at the time!). So if you take Metformin and eat a high-carb diet, unfortunately those carbs will tend to "go right through you" as well.
Eating fewer carbs is the most important thing you can do to stave off digestive effects of Metformin. Other things you can do include not taking it on an empty stomach, starting on a small dose and working your way up, and taking it spread out over the day (this won't affect how long the drug is in play, since as I said above it takes weeks to build up, but it does affect how much of it your stomach is dealing with at any one time). The XR version is another of these smaller steps that can help make it gentler on your stomach, but the best thing you can do is to reduce carbs. Not down to zero or anything, but just bear in mind that high-carb foods do contribute to Metformin side effects being worse.