Save as HD movie vs movie

I downloaded a 720p video from a URL using QuickTime, and then saved the file -- first as a 720p HD QuickTime movie, and then as a regular QuickTime movie. Both files seem to have the same dimensions and to be of similar quality, but the HD video file is over 1.1 GB in size and the other file is only 444 MB.
Beyond the HD movie taking up more disk space, is there a difference between the two that I'm missing?
Here's the URL for the original file:
http://tinyurl.com/37j5lpb

so the re-compressed file has a higher data rate, but isn't necessarily of any higher quality than the file created using 'save as ...> movie." right?
That is essentially correct. In the first case ("Save As... > Movie") the actually data is the same as the original source file--just copied to a new container. You can think of it as pouring milk out of its original carton into a cup or glass. The milk remains the same even though it is now in a different container. On the other hand, re-compressing the file always has the potential for degrading the data further. Since a transcoded/re-compressed file will never be better than the original (i.e., you can't create "new" data to replace that which is/was thrown away by compression), it might be more appropriate to speak in terms of "retention of quality" rather than use relative terms of better or lesser quality.
Basically, H.264/AAC is a very efficient/scalable codec with a very wide range of useable data rate. Thus, at low data rate it provides reasonable quality and very small file size. At moderate data rates it provides reasonably good quality in a moderate sized file, and using an unlimited data rate, it retains nearly all of the original source quality in a comparatively larger file. The 5 Mbps video data rate is well suited for 720p (1280x720) files. Compare this with codecs like DV which use 25 Mbps for SD video content which displays at either 640x480 or 853x480 display dimensions. And, when compressed at 1.6 to 2.2 Mbps, usually provides DVD-like quality roughly equivalent to MPEG-2 content compressed in the 5-8 Mbps range.
As a rule of thumb, it is usually best to retained the original data in its original compression format if it is already highly compressed and is already compatible for your use. Where the original file is in a format not already compatible for use by you or is in a compression format having a high a data rate rate/file size too large for your purpose (i.e., you would not normally post a DV file to your web site on the internet when you could post a much smaller file of similar quality), you would convert the file using a compression format and data rate better suited to your particular work flow.
the two files are of different sizes because the HD file has been forced into a particular format that has uses a particular (higher) data rate?
That is correct. Basically the file size is directly proportional to the data rate at which it is encoded. (I.e. data rate per unit of time multiplied by the duration of the video in units of time equals the total amount of data or file size.)

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