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I have put together a rather large script file that does a lot of math. It seems to me that if I place a script variable value on the spreadsheet (setValues()), the whole spreadsheet recalcs (i.e.; it takes awhile to refresh). Is that true?

What if I want to format a cell from script (e.g.; change a number cell to a percentage cell with 3 places)[FormattedSS.getRange(rangecoordinates).setNumberFormat("#.###%");]? When I set the format, does the whole spreadsheet recalculate?

I am new to Google Sheets. In Excel, I could set calculation off. Google sheets does not seem to have that option.

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Google sheets has no manual calculation option. You would need to create a formula to check whether to run the rest of the formula. If the output is a single cell you can easily use a circular reference to retain the value.

When it comes to Google App Scripts every time you execute a script there will be an annoying delay, that is just how it works, the App Script should be avoided at all cost in a normal spreadsheet except for when actually necessary.

Google App Script Server -> Google Sheet (delay to send information back and forth)

Google Sheet always recalculates after any change