The patch prevents REGENV from wiping AUTOEXEC.BAT and CONFIG.SYS on every boot, instead it is given alternate files to mess with leaving originals alone. No compatibility problems will arise but you do want to include the data in original files into the new ones (bunch of SET directives IIRC).
Rest is using MSDOS.SYS and COMMAND.COM from an alternate source that allows alternate boot modes and there's no problems with that either.

Thanks. The only difference that I have noticed so far is that the high/upper memory management is different in the ME DOS environment - no more HIMEM.SYS for example. Maybe that can cause problems with older software ?

You no longer get an option to load your own HIMEM.SYS equivalent, it is part of MSDOS.SYS and loaded automatically. You can still add the line in your CONFIG.SYS with desired parameters however.

That does not work here, results in a boot error+beep. It is also not possible to load EMM386, then the system hangs. Do you know if there is an article about configuring config.sys\autoexec.bat under Windows ME somewhere on-line ?

Should be possible to get the DOS mode in the boot menu. Similar to what 98 does. Entrys like "normal start", "safe mode" "command line only", "command line with netwirking", etc
Those later entries is what you want.

It boots directly into DOS => C:\ when WIN.COM is not started in the AUTOEXEC.BAT
i am more interested in how for example high memory is handled and if it can be configured or has to be configured. The LH commands seem(?) to work though.