One of the new features of Windows 8.1 is automatic DPI scaling (Microsoft calls it per-display DPI scaling). What is meant by that is that Windows 8.1 will automatically select a DPI scaling for each connected monitor. So, the Surface Pro would be run at 150% while the larger Full HD monitor on your desktop would run on 100% (or whatever the appropriate value is) without the two values interfering with each other in any way.
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See also: How to Change DPI Scaling Size for Displays in Windows 8.1