Thank you for your participation on this valuable discussion. The first screenshot you showed previous version had some valid issues - because
1. little space left for Modifiers/Toppings and
2. there were no Grouping tabs for modifiers.

However new version solved them. Every Modifier Group now has a 24-30 modifiers shown per group without any scroll bar. If you need to show "No Onion" or "Extra Onion" ..Multiplier is life saver.

In addition to that you can create new set of modifiers and arrange them in group. You can create Groups like "Standard Mod", "Expensive Mods" and so on.

Another trick is to add more multiplier buttons like "Half-Reg" "Half-Deluxe" . So half regular will cost 0.50 and may be deluxe will be 0.60 .

Current system has been tested in our known stores. If any one needs more customized UI, we say its not a bug. rather it should be posted in "Improvement suggestion" section. We will consider that in some next releases. In case of time constraint can go for https://orocube.com paid customization.