MAME, when outputting "native" video, really does just output video exactly how the original board did. This means that there are some rather large variances in number of active vs. blank lines, porch widths, sync widths, etc. Some digital monitors have a lot of "memories" and will hold settings for your most commonly used games, but many only have one or two memories per resolution (e.g. there may be a memory for 14-15k, one for 15.1-16k, one for 23-24k, one for 25-26k, etc.). If you only play a few games, this may work for you, but if you play lots of games, you may still end up adjusting frequently. YMMV.
Remember, the monitor only knows a few things about your video. It does NOT know what game you're playing. Many games are indistinguishable from the data the monitor knows but have differing blank areas.
The reason for older monitors not having separate "memories" is that their "memory" for settings is physical knobs and dials. Things change when you physically move them.
There are some nifty tricks you can do to "box in" the video to try to make everything about the same without sacrificing "nativeness", but you'd have to configure that.
Disclaimer: I don't run MAME. Real game hardware all the way

I do frequently swap boards, though, and yes, I do have to re-adjust even my digital monitors for most of them.