Batch Action set - can not suppress dialog

Actions explicitly record the absolute alpha channel name, which can create multiple issues when automating.

Scripts don't have this limitation.

This code removes all channels (alpha or spot, but not layer mask alpha channels):

#target photoshop
try {
    activeDocument.channels.removeAll();
} catch (e) {}

And this one only removes alphas:

/*
https://community.adobe.com/t5/photoshop/remove-alpha-channel-during-a-batch/m-p/11285697
*/

#target photoshop

removeAllAlphaChannelsNotSpot();

function removeAllAlphaChannelsNotSpot() {
    try {
        var myChannel = app.activeDocument.channels;
        for (n = myChannel.length - 1; n >= 0; n--) {
            aC = myChannel[n];
            if (aC.kind == "ChannelType.MASKEDAREA" || aC.kind == "ChannelType.SELECTEDAREA") {
                aC.remove()
            }
        }
    } catch (e) {}
}

While this code only removes spot channels:

/*
https://community.adobe.com/t5/photoshop/remove-alpha-channel-during-a-batch/m-p/11285697
*/

#target photoshop

removeAllSpotChannelsNotAlpha();

function removeAllSpotChannelsNotAlpha() {
    try {
        var myChannel = app.activeDocument.channels;
        for (n = myChannel.length - 1; n >= 0; n--) {
            aC = myChannel[n];
            if (aC.kind == "ChannelType.SPOTCOLOR") {
                aC.remove();
            }
        }
    } catch (e) {}
}

https://prepression.blogspot.com/2017/11/downloading-and-installing-adobe-scripts.html

Have you tried with Conditional action, actually step which will determine which action to play > condition : Document Has Alpha Channels to run action with remove alpha channel step (Then Play Action) or Else Play Action without step to remove alpha channel.