It doesn't matter whether the source files are lossy (eg mp3) or lossless (eg FLAC), they'll be the same size when decoded to PCM format as per the Red Book standard for audio CDs - 16 bits per sample, 44.1KHz sample rate, which for a stereo track translates to a constant (and non-adjustable) bitrate of 1411Kbps. There's no difference in subjective sound quality between burning apps; either the bitstream is decoded and burnt correctly or isn't, although IIRC (long time since I burnt an audio CD) some apps may want to insert a 2-sec gap between tracks unless you specifically tell them not to.
The quality (in theory at least) will however still vary depending on the source files - with lossy compression, some of the audio data will have been chucked away and replaced with noise (which is more easily compressible), whereas an audio CD-R burnt from decompressed FLAC or other lossless files should be bit-identical to the original source CD as long as there were no errors in the ripping process, at least if you discount possible minor differences caused by the differences in drive offsets (which are for the most part unimportant).
