The context for that quote, is that an individual was arrested for Misdemeanor Assault on a federal officer, specifically due to shining laser pointers at their eyes. Upon physical search of the individual, it was found he was, "carrying a machete, a large mortar firework and a section of galvanized pipe with endcaps and fuze assembly". Lastly, and likely most importantly, the individual consented to his phone being searched.
Now, to the original quote: "CTD is sending Fly Team Agents to cover the interviews of individuals arrested during the night and early-morning hours this weekend. They will also conduct initial exploitation of phones, or other communication devices they are carrying. These Agents may uncover a situation like the one described in the previous paragraph...".
There is nothing in here that implies they intended to search the phones without a search warrant of consent. Law enforcement officals do not make it a routine matter to specify, "They will also conduct initial exploitation of phones, or other communication devices they are carrying once they have a search warrant or consent from the individual". That would be equivalent to me saying to a SWE, "I need you to go and complete X task", then qualifying it with, "and make sure you do x, y, z, a, b, c task that I already know you know and were taught to do".
The title of this article should really read, "FBI Team Sent to 'Exploit' Criminal's Phones in Portland". The fact that the individual(s) also happened to be protestors, is really irrelevant and highly connotative. There is nothing in the First Amendment that gives someone the right to threaten and/or carry out actual violence against another individual, nor should it allow for that. Not to mention, there are specific Federal statutes regarding assault against federal officials.
Frankly, if I was a protestor exercising my First Amendment rights, I'd be pissed that someone was carrying what appears to be a pipe-bomb to what was supposed to be a peaceful protest.