Nick--
http://flac.sourceforge.netHere you can learn all about flac directly from the source. If you search, you will find definitive answers to all your questions. For somewhat mangled and incomplete answers, read on.
First of all, you should check the "compression" setting both on the MC converter and the others. There is no compression involved, but that setting determines how hard the encoder will work looking for ways to make the file (losslessly) smaller. If, for example, you have MC set to 8 and another set to 1, you would see a significant difference right there. As an aside, there is no increase in CPU load to decode either setting on playback.
Barring that, here's what I know (and so much more) about your questions:
1. Verify is writing bits and then reading them, serially. I've used it both ways and found about a 30% difference in time. I have never found an encoding error either way (apart from a 1-hour drama one morning when I tried a non-released alpha version of the plugin for scthom). My confidence in FLAC and in scthom's plugins is very high.
2 and 3: I know enough to direct you to the plugins page where you can read it directly from scthom. I use both these settings enabled, altough eartlier encoders didn't have the option. Note that all files encoded either way play fine and the data integrity is NEVER affected.
I play FLACS encoded within MC from each of the various versions and with all combinations of settings present in encoding. Additionally, I have FLACs encoded through dbPoweramp and from unknown provenance (etree.org). All play perfectly and all decode properly to WAV when I periodically check them.
I've never seen anything like the 90-secs its taking you, but I've never converted from APE and, IMO, that end of things might be worth checking also.