Not sure what you mean here. Convert and / or Rip to FLAC has been there since at least version 17 (When I started using MC)
The OP means when burning a data disc. You can only set it to automatically convert to MP3 or WMA, not any other formats. I see why it has the convert to MP3 (for MP3-CD playing devices in days of Yore) but I can't imagine the need to convert to FLAC on the fly when burning data discs is a common need.
I can't even imagine that the entire burn to disc function is a common need anymore, frankly.
In any case, that isn't available now. If your source formats are FLAC, then it'll use those if you just leave it to original. If your source formats are not FLAC, and you need to do this a bunch, just convert them to FLAC for good, would be my choice. If you really don't want to do that for some reason, but you need to burn some discs, you can also create FLAC copies in a variety of ways, including creating a Handheld or just using the built-in Convert Format system. You could convert them and have it make copies and stack them with the originals, and then use those copies whenever you need to burn them.
Option to update the source location for multiple tracks.
No idea what this means.
Can we have option to skip conversion for certain file extesnion
The Handheld converter can do this. You can set up any filesystem location as a handheld, so you could do it as a two-step process. Convert your files to a Handheld (perhaps using a playlist as a source, so you can easily build the list of files to burn) and then run the handheld sync to make a folder full of files which you can then burn to disc.
See more:
http://wiki.jriver.com/index.php/Handhelds