Especially in the short program, it's almost a norm that a skater who ruins the combo at the beginning later adds an extra jump to the other individual jump. It's way rarer when a skater forgets to do so.
Yes, in senior short programs (and lower levels, but not junior), it's very common for skaters to have a "plan B" to try the combination as the first non-axel jump and if they don't manage to include a second jump there it's a wise plan to add a combination, usually double toe, on the second non-axel jump.
Especially since the rules stopped requiring the solo jump to be preceded by steps or other skating movements. When that was still a requirement, to make best use of this plan B the skater would need to plan some preceding steps/moves before both non-axel jumps, or else they risked taking a smaller deduction for the lack of steps before the originally planned combination. Although if the reason they couldn't do the combination was because they fell, they were already going to take the maximum deduction on that element anyway.
In
junior short programs, the solo jump has a required takeoff. They can't just add a combination to the only jump with the required takeoff, because then it becomes "not according to requirements" and takes a -5 GOE reduction for that reason, while the non-required takeoff without a combo will still be called as the combo and also get the -5 reduction.
The only way a skater could take advantage of the "add a combo to the solo jump" strategy in juniors would be to plan a triple of the required takeoff as the combination and a double of the same takeoff as the solo jump later (or vice versa for junior women). For most skaters that's a bad strategy to try to maximize intended base value.
What gets trickier is trying to add a combination to an axel-type jump in the short program. A solo axel jump is required in all short programs. For seniors (and for junior men), either double or triple axel can fulfill that requirement. So it is possible to plan (initially, or as plan B) a 3A combination and a solo 2A, or as in the example cited above to go to a plan B that treats a popped axel attempt as the required solo (as if it were planned as double) and to add a 3A combination later as the combo jump.
But what skaters need to be aware of is that if they fail to include a combo on an earlier jump, they must not add one to the only axel in the program. As with the specified takeoff of the junior solo jump, that will get them "not according to requirements" deductions on two different elements and no credit for the second jump in the improvised combo, instead of just the loss of points on the jump they missed.
It's always best to have
specific backup plans for each potential error on the first jump or two in the SP. Trying to wing it without planning in advance is always risky.
In the free skate there are more potential variations of where things can go wrong and in most cases where they can be made up.
So yes, it's easier to lose track of all the potential options. The main things that the skater needs to keep in mind are that there must be an axel of some kind somewhere in the program, there can be a maximum of three combos, no jump can count more than twice, and that any triple or quad that's repeated needs to be in combination at least one of the two times in order to earn full credit for both.
As mentioned, with the current rules, getting the +REP designation for a repeated triple/quad with neither in combo is a partial loss of points but not as severe as other potential rule violations.
If the supposed "clean program bonus" would encourage skaters to schedule less difficult programs even though they would be able to do more difficult elements, then there could be situations i.e. when a skater with a fall who has already jumped 3Lz replaces i.e. 3S with 4Lz - even if he falls, he can still hope for better point value than 3S would bring.
Only if he has a good chance of actually rotating that 4Lz attempt.
If it ends up being downgraded (as is more likely later in the program when the skater is tired, and from an approach it hadn't been trained for), then fall or no fall it will end up being worth less than a clean 3S.
Of course, it means that alternative program planning might be necessary
Certainly adding such a bonus would change skaters' strategies both for initial program layout and for potential backup plans.