Is it possible to use a custom loading indicator in place of the Skuid provided indicator?

Do you mean the "Please wait" message in the block UI? If so, then yes you can! That takes html, so you have a lot of freedom with what it shows. We use something like this for one of our pages that takes a while to load...

<div><h1>Please wait...</h1></div><p/><img src='https://i.imgur.com/47uRojE.gif' width="300px"/>

Just put it in the message for the action.

Josef, if you're talking about the placeholder "spinner" that shows up when loading Skuid in Lightning Experience, then the answer is yes, you can configure this by going to Skuid Settings, Org Preferences, Lightning Pages / Apps, and then enter the Name of a Static Resource containing an Image file that you would like to use as a custom loading indicator.