Why aren't they add-ons?
You can change the fee, chips, rake, etc, and any individual add-on. The values for add-ons defined on the Game tab are the default values. Those values will show up in the Add-on dialog when you purchase an add-on, but they can be modified at that time.
If you have a known set of "top-ups" a player can do, you can create profiles for them to make it even easier. For example, assume players could top-up for $2K, $5K, or $10K only. You could create Add-on Profiles for each of those values. Then, when adding-on (or topping-up), you only have to select $2K, $5K, or $10K from a pre-defined list. This is particularly helpful when players receive differing numbers of chips and/or the add-on is raked different amounts. On the other hand, if you allow players to top-up for whatever values they want, this might be more of a hassle than it's worth.