I'm not sure about this message. You can not modify the layout in Filemaker Go.
You may have changed to a font that is not supported by Go and Go is changing the font to a support font and this is the reason the message is showing. I guessing here. This is where I would start testing. Filemaker employees do review comments on here, but I don't know if they work weekends.
This link is to the development Guide which list supported fonts.
You will have to design layouts to fit the iPad screen. Databases do not automatically resize. You can take a look at the starter solutions for examples of different layouts. (Desktop/iPad/Iphone)
I think that this message will only appear on an iOS device when the following is true:
The iOS device is a client of a hosted database--it's not a file stored on the local device. (But I could be wrong about this.)
The file is open with a Full Access privilege set. (This is also the case if no password protection has been set up for the file.)
You are changing the View options (View as List, View as Table, View as Form). When a fileMaker Pro or FIleMaker GO client of a hosted database changes the view, this message appears asking you if all other users should also get this new view the next time that they go to this layout or if this change is just temporary.
If you don't change the view, I doubt that you'll get this message in FM GO. One way to avoid getting it, it to set up different layouts for each permitted view option and change layouts in order to change the view.