Is there a way to turn off Flatten/Don't Flatten, Merge/Don't Merge, and Rasterize/Don't Rasterize

Most action step the have dialogs have the setting you used recording the step recorded into the action step and when the step is played the recorded settings are used the step bypasses displaying its dialog. You can check the show dialog check box on the left side of the step to have the step show its dialog. If you check that box the step will be interactive the dialog will be displayed with the recorded settings set.  You can Accept them of change them.  However, if  you insert a step like open. The open step will be interactive and open will show its dialog there are no settings that can be recorded into the action.  If you record open a particular file the open step will not be interactive unless you check the show dialog box .  Also if you Run a script menu File>Scripts>Script Name  in the action if the script has a dialog and it is not a Plug-in the script dialog will be interactivity displayed when the step is played. If the script is a Photoshop Plug-in the script will record the setting you used recording the step into the action step. The dialog will not displays when the step is played unless you tic the show dialog box on the  step's left side.  Actions the that have interactive steps should not be batched an interactive step stops the batch process user intervention is required. If  record Flatten Image or you insert menu item >Layer>Flatten Image a Flatten Image step should be added to the action.  Flatten Image, Merge Down and Merge visible do not have a dialog.   So the dialog you are seeing  is most likely form some kind  Photoshop conversion step.  Like the action targets several layers and is then converting then or combine them with some Photoshop feature.  Or you are changing  document mode to something like multichannel which requites some conversions where the resulting conversion may differ depending on how layers are combined. You may need to use a different sequence of steps so there is nothing ambiguous so Photoshop will  not have to prompt the user for how they want the conversion performed.  What you seem to be seeing are more prompt than dialogs you are not filling in settings  or values or checking  option.  You are being asked how you want the conversion done you may get different results if you want to preserve  or shapes.  You may need to flatten or merge layers into a smart object so there is only a single layer the conversion is dealing with.  You have preserved your layers shapes text etc in the smart object  the document is effectively flattened  when you converted all into a smart object.  You can open the smart object and get all your layer back.   

Impossible to know without understanding the steps in your actions. Some of those instances may be possible to bypass like with the old insert empty layer & merge trick or using specific tools. if it's more complex than that, I guess you will have to venture into scripting.

Mylenium