Ferrite bead for high-speed digital IC
Ferrite beads used to isolate local power supply nets have two effects:


Prevent noise from the main power supply net from reaching the isolated chip.
Prevent noise generated by the isolated chip from reaching the main power supply net.


As the link you provided, and the Howard Johnson article linked from there, say, if the first effect is desired then isolating different chips with ferrites is likely to be overall counterproductive.

I'd recommend to use ferrites mainly when the 2nd effect is desired. For example, you have a high speed processor on the same board as a sensitive analog circuit. Use a ferrite to isolate the power supply of the processor so that it's simultaneous switching noise (SSN) doesn't impact the sensitivity of the analog circuit.

In this case, the ferrite will in fact increase the noise seen by the processor. If the noise is not excessive, this may have no impact on the processor performance at all. If necessary, you can use multiple bypass capacitors in parallel, reverse-geometry capacitors, etc. to achieve lower impedance between power and ground and mitigate the negative effects of isolating the supply.

In case the analog circuit does not produce substantial SSN itself, it may also be helpful to isolate the analog circuit behind a ferrite. This is essentially what's described in the "When to use them" section of the TI article.

If in doubt, you should use a simulator to design your power bypassing and decoupling network, being careful to include all important parasitic effects of your capacitors and ferrites. You want to design the network to have a low impedance when driven by a current source in place of any of the SSN-producing chips; and to have a low transfer impedance from any SSN-producing chip to the supply of any sensitive circuit.