Even if 18F is paid out if other agencies budgets, Congress could as easily prohibit those agencies (or GSA itself) from spending any money on 18F. Heck, Congress could directly restructure, break up, or abolish the GSA.

Or, they could exercise the recently-revived Holman Rule and simply cut the pay of every individual (or select individuals) working in 18F to $1/annum. If you work for the Federal government other than in an office with special Constitutional protection, no matter what the notional funding structure of your particular unit, your job, pay, and benefits are not protected against Congressional action, and you should not be misled to think that they are.