Hello buzzgary, 

Here are the answers to your questions: 

1.Show/hide all markup with one shortcut key -- e.g. all sticky notes, markup circles, comment text for markup circles. How can I do this?

Sorry that Mockplus RP does have any shortcut key to show or hide any sticky notes, markup circles or comment texts and more similar components. 

But, you can try to show or hide them separately on the right property panel: 

Or you can try to add all comments, markups or explaination outside the artboard.

You can easily select the option saying "Show content outside artboard" to show them all up at one when previewing the project: 

2.Have the bold blue underline in tab bars be full-width when the label is longer than the "item 1" default text. Right now the bar is much smaller than long tab bar labels.

Right click that tab bar component to select "Advanced edit", you can easily select that label layer to stretch the underline. 

3.Create design alternates for certain artboards/screens and substitute/promote the alternates to official to see how they will change the feel of certain flows.

Do you mean to create a page state or something else? If you do mean that, Mockplus does not support creating page states yet, but you can try to create different pages with different content to check that overall feel.

4.Create different flows using the existing artboards; have conditional logic (can be manually selected; but can be scripted as well) when a component is clicked.

You can easily create users flows using the existing artboards with drag-and-drop and add descriptions to the connectors. Here is the tutorial that can help you learn more: https://help.mockplus.com/p/256

Please let us know if you need any further assistance.