I'll have to echo Bashar here. The advantages of resizing outweigh the advantages of leaving everything at 720x480.
But to answer your questions:
what if I wanted to send in a lossless copy to a convention? I'm not able to set the flag with these types of codecs, correct? So basically I would either HAVE to resize before I sent it in or make it clear to them that when they encode it it needs the 4:3flag
Technically, it can be done... I mean, I
have seen people try to flag their old XviD.avi files... but it just leads to more headache than it's worth because not all players support .avi flags. So, I'll just say: no. You can't flag your lossless files. (I think .avi flagging is something specific to XviD anyways. IIRC the container is supposed to determines AR flagging, and I don't think .avi is made for that unlike .mp4 Anyone correct me if I'm wrong...). I've also seen people send lossless files to a convention with clear instructions on what AR to use, and the con still fucks it up. And trust me, you don't want to be sitting in the audience --the proud creator of your work-- and see it shown in front of a packed room of rabid anime fans with the wrong AR. You don't want to be the guy running the contest either. I'm not saying that has happened to me, but I can sympathize.
So just do everyone a favour, and resize your footage. Ideally before starting your AMV, but at least afterwards if sending to a con.
Also, if I created lossless versions of my footage at 720x480 and imported that footage into my NLE with the right setup (accounting for the 0.9PAR every step of the way as Bashar put it) wouldn't my graphics stay how I imagined them in the first place? I'm pretty sure Premiere can stretch or shrink the footage to look right during editing so any effects added would look right with a 4:3flag attached to it in the final encode (just like the footage).
If your NLE is smart, it will TRY to compensate for the AR stretch, but sometimes it cannot do that, especially if you create custom graphics. An image that was nice and clean with crisp edges may become warped in the end due to asymmetrical stretching, unless you had enough foresight to squeeze each and every graphic beforehand so that it looks correct when stretched in the end. This is most evident for text. See, text is special in the sense that it has to be pixel-accurate to look correct. So, even the slightest resize messes with that pixel accuracy, and it may wind up looking like shit. NLEs can compensate for that by softening the graphic/text, but personally I would rather have crisp clear edges, which is achieved if you just resize to the proper AR, and use square pixels the whole way through.
Now, comes the tradoff. As stated earlier:
any time you resize, you lose
some quality, (because you are altering the pixel-accuracy... and sometimes detail really is that fine... though rarely...) so some people just like leaving it at 720x480 so the footage is completely unaltered. Yet, I would like to think the advantages described so far outweigh that. If not, here's three more: 1.) The 'extra' quality you gain by leaving your footage at native res will likely be lost when encoding your final AMV, unless using quality settings that you probably shouldn't be using in the first place. 2.) By resizing, it can act as a slight cleaning step by softening out fine noise in your footage. 3.) If you add effects/colour correction/sharpening/cleaning/panning/zooming, most quality you think you gain by not resizing will be lost anyway...
So yeah, you can totally leave it at native res if you want, but resizing beforehand just seems like the better option to me; at least when making an AMV; encoding for quality-sake is a bit of a different story though.
