I have to admit, I don't remember how it used to work in XCom, but intercepting small UFOs after the "one timer to rule them all" nightly has become nigh impossible.
Sending just one interceptor on a very small UFO, the best result I have had was a few cannon shots at it. Most of the time, the window pops up, I click aggressive, disable missiles (I want it to crash) and the UFO doesn't even come close to cannon range.
Does waiting at full range with the window minimized count as "intercepting"? I have had even less success getting two interceptors on a UFO than one. When I have attempted that, by the time I get my 2nd interceptor on a UFO, click aggressive, maximize my first interceptor and click aggressive, the UFO disengages within seconds. Interestingly, it disengages from both crafts at the same time, even though the first interceptor's interception window has been up for longer.
If you try to call the attack as soon as a window pops, to kind of send interceptors in waves, it's impossible to get more than one interception because you can't minimize the interception window so "geoscape time" doesn't tick so the 2nd interceptor can't catch up.
As I said, I don't remember vanilla XCom, but the behavior changed rather radically with that commit.