Why not place both options explicitly in the schematic and pcb side and set one of them as DNP in the bom? This would ensure that anybody reading your schematic/pcb will know what you where doing including you in 5 years.
This is for an old schematic design that I’m using for analog synths. I’m actually somewhat keen to keep the schematics intact and have even explicitly annotated to match the original. That so I can use forums for these designs and talk about things like R3, Q1 if (or when really) I need to troubleshoot
I’d really like to keep the schematic as is and just make a footprint where I can either populate an smd dual or two matched TO-92’s. I’m pretty sure I’ve seen other PCB’s do combos like that before…? Maybe they did explicitly in the schematic, I don’t know…
Also seemed like a fun thing to do, I’m all about learning
Well give the alternative parts a reference outside the range of the ones normally used (example add a prefix letter like QA1 or add a number prefix/suffix)
Of course you can bodge it on the pcb side but future you will pay the price for it. (The clean way is what i suggest. You can do it your way but that will make your life harder in future. And i doubt it makes life easy now to be honest.)
If you still want to use the bodge on the footprint side then give the pads that need to be connected the same pad number. That way pcb_new will want them to be connected and you can use normal traces to do it on the pcb side.
Just to be sure, also add TO-3 and TO220 footprints.
For long-tailed pairs or other circuits where tempature differences between transistors are important, using TO-92 is not a very good option, (Neither is SOT-23).
With TO-92 there is a lot of insulating epoxy between the dies, and even if you wrap some copper wire around bouth packages the coupling is not very great.
You can easily get different temperatures bedause of heat conducted through the pins. Power transistors with a metal backside can have much better thermal coupling between them.
In KiCad you can add “custom graphics” to a pad. You’ll need to do a bit of experimenting to get the details right though.