Yellow and white show well on black. The really aren't far off in contrasting black.
Your difference is bleed. If you had yellow on yellow, the bleed would be very close to yellow on white. A more opaque surface than on clear where you simply have yellow on black. (Think about painting, one has white primer, one has black primer, now topcoat yellow. You'll have two different shades of yellow. Add another yellow coat to both, now they are similar.
You need an ink with more pigment for printing on clear without bleed.
If your printer registers (aligns) well, you might be able to double print to get a more opaque yellow,
Or.. print yellow one point smaller; reprint over it at 100%.
The difference between will be in the edges. (letter spaces would be off on long words, It may limit how many letters you can print on one sheet or at one time without bad register.
A brighter yellow may help on clear.
The blacking out of white would be easiest, but not best. Now you have two shades of black going.
Also, some folk look more for crispness in outline, some look more at color consistency. You may have to decide.
If you ever saw how many proofs a graphic artist/printer makes sometimes to get it "right" vs "ok" you might get why the suicide rate runs high in the profession. It isn't even the artist deciding sometimes, and never for final. Its approved or not by the customer in the end.
Testing is key, try a small one both ways and hold them there side by side on black paper, shirt, or whatever to decide
