Personally, I don't know why you wouldn't want it to start at boot. My answer deviates slightly from the MySQL tag and talks about databases in general.
When you say you want to check consistency - is this for physical corruption or logical corruption? If something's physically corrupt, there's a very good chance it won't start anyway. If it's logically corrupt, unless you have a specific maintenance program that knows the structure of the database and what relates to what, I think you'll have a hard time manually ensuring it's logically consistent (by that I mean transactionally consistent). If the database is any good, it will do some form of transaction logging anyway to guarantee transactional consistency.
If you have hardware that corrupts things (but only on boot) you have bigger problems which need to be resolved. Equally if you have flakey network connections, you have other problems. Networking starts very early in the OS loading process, and once it's up it stays up until told otherwise.
Think of what happens if your Exchange server or SQL Server reboots at 3AM on Saturday morning and for whatever reason you are unable to get to the server and start the databases manually. Until you tend to the server, it won't accept emails or your website is down for hours when it could be up and running again by itself in the time it takes the server to reboot.