That's what I was thinking, but sometimes you get several more lines of a given stage, or you get to see the bottom tiles entirely instead of them being cut off. I've become used to doing maps where tiles are fully visible (when possible), so if the bottom row of tiles is missing 2 lines of pixels, I try my best to fill them in and if showing everything makes it easier, then so much the better.
Besides, as for junk showing up, many games tend to show wrong colors along the edges of the screen when scrolling, probably an artifact of the way the NES deals with tile colors, something you almost never see on a real TV because the right and left edges can sometimes be cut too. In fact, in FCE Ultra you have the option to clip the leftmost and rightmost 8 pixels although this isn't enabled by default unlike the top/bottom thing.
Personally, the more you show me, the happier I am. I almost always have to crop screenshots when making a map anyway, so it's not like it would give me additional work.
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"With the first link, the chain is forged. The first speech censored, the first thought forbidden, the first freedom denied, chains us all irrevocably." [...] The first time any man's freedom is trodden on, we're all damaged. - Captain Jean-Luc Picard
B*tch, meet reality. Reality, meet b*tch. - Me