(1) Are you saying that I could run my entire FLAC collection through this tool to generate MP3s via LAME, in the same folder structure?
(2) Does the version of LAME matter? I prefer to use halb27's 3.100m variant, with the switches -V0 -cvbr 3 -Y --lowpass -1. Some of those are switches not available in the latest release, 3.99.5.
(3) Are all tags automatically transferred from the APE-type stored in a FLAC container to ID3v2 compatible ones, including album art and lyrics?
(4) Is there any way to also have the software run MP3Packer after LAME has completed? How about MP3Gain? (Halb27's variant runs MP3Packer automatically, but the standard version doesn't. It might be a good addition.)
(5) Is there any way to also copy JPG/PNG files that are stored in the source FLAC directories to the destination MP3 directories?
The Encoder Options window doesn't currently get set by the command-line options; it's only the other way around. For instance, if you change the target to Bitrate, the slider is at 192 by default, so it will generate the command line "--abr 192".
Having both "Extensions to ignore" and "Extensions to copy" was a feature specifically requested by another user.
I actually implemented it to see if the string ends with the string specified, rather than purely checking for extensions, and the copy list overrides the ignore list. Because of this, you can copy "cover.jpg" while ignoring "jpg", and it will work the way you want. I know that's not clear just from the interface, but hopefully that means it's useful to you.
In the meantime before I get around to implementing the full tagging feature you requested, can you tell me if there's a specific tag you'd like to carry over? So far I've just implemented tags that LAME officially supports; the only TXXX tag I've put in is ReplayGain, and that's not enabled by default.