IMO the single-sequence method is the only sensible way, but it's missing proper song parts and an overview etc. that there is in the Force sequencer. Not really knowing how proper it is, just seen a few videos.
Actually, I don't recall ever seeing a really good song support in any sequencer, software or hardware, notation program or anything. They're always based on song parts starting razor-sharp from one atomic point, when in reality, there are anticipating changes, transitions, sort of like pick-up bars (not meaning the sort where you pick up women). The same with melodies. The only thing that comes close is some arranger keyboards that have "fill-in and move to variation X", which have transitions to a certain rhythm variation. And so there could be different transitions from verse to chorus, from chorus to chorus, from chorus to verse, from bridge to chorus, etc. In a sequencer, this would require support for overlapping blocks. Or like, if the lead vocal of the chorus starts one single 1/8th note before the first beat, you have to dedicate an entire bar for that. When it should overlap, like negative time, pre-roll bar -1 that the sequencer would play when receiving the "switch to chorus" instruction, if it has enough time. If it's too late, then at least play as much of the pre-roll bar as possible - but only on those instruments that have that pre-roll.
Non-destructive pattern changes would be good as well, for example change kick/snare pattern to half-time or double time, but keep hi-hat/ride the same. The software should be open source, so I would code my own features.
