(Before I get started on my rant, I want to point out to anyone who wants to reply before reading my whole comment that I realize my experience is limited and my needs probably differ from yours. That being said, here I go...)
That's actually my experience with most easy-admin tools. They expect config files to follow very specific (and undocumented!) forms; they never have the parsing flexibility of the programs that actually read those configfiles. So, it's hands-off /etc---either do it with the easy-admin tool, or don't do it at all, because once you touch the file manually in a way the easy-admin tool doesn't expect (though it might be a perfectly valid way according to the manpages of the corresponding programs), you'll be reverting your config. Run into a limit of the easy-admin tool? No more easy administration for you---either you can try to patch the easy-admin tool (most I've seen suffer from a lack of documentation), or you can remember to never, ever use the easy-admin tool to modify certain things again, lest you hose the hand-edited config (thank god for chattr-immutable, at least).
Now, I haven't surveyed many of these tools, nor have I kept up to date on them. What I describe is what was shipping with major linux distros a few years back. It's quite possible that there's a tool out there that:
(1) is designed from the start to notice inconsistencies between its own set of config data and the files it's modifying in /etc, aborting before anything gets hosed;
(2) implements flexible and tweakable parsing strategies that are well-documented, so you know what you can and cannot do when hand-editing things in /etc;
(3) has well-commented, modular code, with every script, file, and interface detailed carefully and explicitly in an organized, well-written set of manpages; and,
(4) provides a solid cross-reference of every admin-tool-config-variable versus what it tracks in /etc.
IBM's AIX had its own approach to preventing hosed configs: on system startup and reconfigure, lots of /etc was simply overwritten by SMIT. No need to worry about confusing SMIT by hand-editing anything---hand-edits would just be reverted to the data in SMIT's database. Early versions of SMIT were notoriously inflexible, causing a multitude of headaches for AIX3/4(?) admins.
Speaking of SMIT, I should point out that SMIT and other tools (such as HP's SAM and IRIX's config toolsets) were based on easy-admin-interfaces that sat on top of a scriptable engine, so you could still use rsh/ssh, crond, and all the regular approaches to en-masse administration, provided your own scripts called the underlying engine rather than modifying things in /etc directly. You could simply look at the logs produced by SMIT/SAM/etc to make a template for your own scripts. This was a failing point of early linux easy-admin tools---the menu-driven systems didn't spit out a log of all the calls made to the underlying admin-tool scripts, the scriptable CLI engine was poorly documented, or (worse yet) the CLI call syntax was inconsistent from version to version. I did notice improvements in that over time in the linux easy-admin tools.
I have heard some good things about YaST, but I've never looked seriously into using it. For what I do with my systems, slackware's mostly-stays-out-of-your-way approach suits my needs. No, I don't admin a datacenter, just a small very-heterogeneous network, so I do realize that what works well for me isn't often going to be the best choice for others. (And, for those of you who haven't configured a slackware system in a few years, do note that the init-scripts rarely need much editing, as they source most needed info from rc.${whatever}.conf files for each rc.${whatever} script, and most everything that starts a non-trivial daemon has a init.d-style start|stop|status|restart script to facilitate straightforward/clean init-scripts.)