I looked up VFITX. It looks like they pay distributions (i.e. dividends) that are roughly proportional to the expectation of the interest rate over the average maturity of their holdings, so you need to take this into account when considering "what-if". They have paid approximately 1.4% in dividends during 2018. That makes their total losses around 0.6%.

This doesn't fully explain the underperformance of VFITX compared to a 3 year bond (which should have made 8 mo/12 mo * 2% = 1.3% in interest and lost around 0.7% on rising interest rates), a net gain of 0.6%.

So VFITX underperformed a three year bond by 1.2%. 0.13% of this is their management fee (0.2% * 8 mo/12 mo). I'm not able to explain the last 1% of difference.

However, in theory, a bond fund loses just as much value on an interest rate rise as the bonds it is holding lose. In my example above, the bond is worth ~$99 after the increase to a 3% rate, just like the fund. The only difference between the bond and the fund is the choice of when to liquidate or roll.

It's possible that VFITX got unlucky on the timing of their bond rolling (see cousin comment).

If you attempted to sell those treasury bonds now on the secondary, you would have to accept the same $99 the shares of VFITX are worth. The immediate, liquid value is the same either way. (You need a common unit to comapre in instead of VFITX in now-$ to bonds in principle-$.)

If you hold the bonds and/or VFITX instead, the interest pay out of the bonds and the distributions of VFITX should also come out equal (except not, the fund has the advantage that it can change its composition from buying/selling bonds, but also has the overhead of selecting and performing those transactions).

(In reference to your below comment, yes, fund != holding bonds. The fund is closer to you buying the bonds, but also buying/selling as bonds mature or you anticipate changes in rates)

You're simply not marking your losses to market - not having a loss here is an accounting fiction, not a real financial difference. In both situations, you have less money than if you'd bought the bonds at a later time instead.