When would anyone ever land the first jump perfectly and decide to turn it into a sequence over a combination unless there was a mistake on the first jump or something didn't quite feel rigth so you decide to play it safe with a sequence?
You wouldn't, if you were planning a combination. Especially in a short program where a true combination is the required element.
So if you take a step in between jumps in the short program, it's obviously a mistake and deserves -2 or -3 GOE, and also being scored as a sequence rather than a combination. (Under the current rules, total value of both jumps multiplied by 0.8 instead of full value; what I'd prefer would be that the sequence loses the combination bonus or gets a smaller bonus, along with the mandatory GOE reduction of at least -2.)
In the long program, sometimes the same kinds of problems cause skaters to add a step in between the jumps of a planned combination as a mistake. If the result meets the rules for a jump sequence (only half a turn on the ice at a time, maintained rhythm), then score it as a sequence rather than a combo, and since sequences are allowed in the LP there's no mandatory GOE reduction but if it looks uncontrolled or like a step out of the landing, then give -1 or -2 as appropriate.
And sometimes skaters do plan jump sequences with falling leafs or the like into toe loops or loops on purpose. It may be because they get so little flow out of the preceding jump even when landed cleanly that they need the extra hop in between to regain momentum for a good double toe.
(I believe this was the case with 13-year-old Michelle Kwan and her lutz sequences in the long program, which were better than her lutz combos in the short that year, and also with broken-toed Kwan in 1998 on one of her two triple loops. In this case, it's worth adding a relatively easy falling leaf-double toe to the end of a triple jump that's hard for the skater to complete in true combination, because that allows her to repeat a difficult triple that she can land cleanly, just not with combo-worthy speed. You'll also see the same reason with many preliminary or pre-juvenile skaters, or even some juveniles and intermediates who are weaker jumpers, who can't yet pull off double-double combinations but can put the double toe in sequence, e.g., axel, falling leaf, double toe.)
Also, skaters might choose to because that's the only way they could put a triple toe as the second jump. E.g., I remember Tonya Harding wasn't doing any combos in her 1994 long program but did have double axel, falling leaf, triple toe. Which allowed her to repeat the triple toe.
Or it may be because they just think that the rhythm of jump-hop-hop-jump perfectly fits the music at a certain point and jump-jump, or solo jump, does not.
Anyway, none of this is about the innovation bonus, which would be for a brand new type of element. My point is that the new system *could*, with fairly minor tweaks, do a lot more than it currently does to avoid cookie-cutter programs and reward creativity in the ways the moves are arranged and combined.
