Of course the fact that the Loser Perp was there at the same time as MB, and that she ended up dead, is a great indicator that LP was the one who killed her.
But it doesn't prove there had to be any prior connection between the two. People do cross paths all the time, with no prior knowledge it will happen.
Most importantly, we have no reason to say LP came there to kill her (or anyone else). That requires knowing what was in his mind when he walked in the door, or before. We don't know that answer. Nor do we see anything in his actions that indicates he was lying in wait, or even expecting her (or anyone). Nor does the costume tell us anything certain other than he wanted to be disguised. Given that he was on a B&E, which brings prison time if you're apprehended, that's certainly enough reason to try to stay unknown.
In fact, him being in a middle-of-nowhere church in the middle of the night hints that there's a good possibility he was there at that hour because he expected to be uninterrupted for many hours.
Given all the above, I think the repeated theme that "she must have been targeted" is an extreme overreach. Is it possible? Sure. But the opposite is just as possible, and likely makes more sense the longer we go, inasmuch as LE has been diligently searching through her friends and acquaintances for over 8 years, and has yet to find anyone that might could have been there, and with motive (to target her), among those who knew her.