Transparently or with minimal fuss?
If you are used to setup and tweak an OS3.x system you will have no real problem working with OS4.1 (or MorphOS 2.7 in this respect). It is still transparent - but, no, it's a similar fuss as you know already from your OS3.x systems. I must admit that both PPC-OS are more mature and "complete" than all 68k-OS I used from the Commodore and H&P era. Nevertheless it's still more work to get them up and running and up-to-date compared to "all-inclusive-gigabyte-DVD"-OS like Linux, MacOS or Windows.
The - for myself - biggest shortcoming is printing. But it's no problem anymore, 'cos I switched already during my 68k-only Amiga area to 100% postscript/PCL network printing and never looked back. I will never ever buy a directly-to-the-computer connected printer anymore. Now everything works just fine with all my systems (OS3.9, OS4.1, MorphOS2.7).