The way to do this has other repercussions because ISBoxer overwrites its own files on every export.
But.
You can copy the C:\Program Files (x86)\InnerSpace\Interface\DefaultSkin.xml file. Call it CustomSkin.xml (or anything else you happen to like).
Edit this file, and at the top is the Default Font item.
You can change the font/size here. Save this file.
Then load InnerSpace, and open the Configuration window (right click, Configuration).
Go to the User Interface tab
Set the Skin XML file option, under the Session side, to point to Interface\CustomSkin.xml
Apply, exit InnerSpace, reload it.
Now, ISBoxer will use the Session values for it's UI. So it does mean that the ISBoxer in game UI, and most other things it displays will be a different font/size depending on what you set, so may no longer fit within the bounds. If you use the in game UI of ISBoxer, this might be a problem for you, so YMMV. BUT, it does affect the popup text too.
Here I've changed the font to Kristen ITC, 24
And Courier, 36
The problem you might now get is that the box is not big enough to display the popup text (I did not with my couple of tests), which you will only find out by testing (I use a DXNothing window for this as it is much faster than exiting and reloading games and the same with InnerSpace as it only seems to read this files during startup - although I probably just lack knowledge of the correct command). This is controlled in the C:\Program Files (x86)\InnerSpace\Scripts\ISBoxerUI.xml file, under the isboxerpopup and isboxerstopup frames. You could change these, but this file is one which gets overwritten on Export from the toolkit, so you would need to have this saved elsewhere and revert to it after every export (and if your games are running you need to reload the team after reverting). There isn't currently an option to use a custom skin for ISBoxer so you would have to persevere with manual handling of the ISBoxerUI.xml. If you have to go down this path, then it may be worthwhile setting up a different font object in the customskin and pointing the popup and stopup frames to use that, so it doesn't affect the other portions of the in game ISBoxer UI.
The downside of changing the Default Font