I'm just starting to experience a cold start rattle... happened this morning actually after the car was sitting for two days. I have a 2015 Prius Three, the EGR system, intake, etc. was cleaned at around 120,000 miles (did it myself, but just can't recall the actual mileage. I now have almost 135,000 miles). In addition, a new PCV was installed, as well as a catch can. Oil is changed at around 7,500 miles, and not losing any oil or any coolant. Also I drive about 85% highway and my daily commute is somewhere around 200 miles per day. Initially turning on the car this morning the rattle was quite bad, immediately shut the car off, started again and had a bit of rattle then it quieted down. I will just have to continue checking on it and seeing if it happens again, as well as checking on the coolant and other items. No codes, but am thinking of buying a new Toyota OEM EGR valve from the TSB kit due to it being much cheaper. Might also look into getting a boroscope or leak down test done just to do additional diagnosis.
The ports were not too clogged when I did the cleaning, but I gave every part and port and passageway an extremely detailed cleaning. Everything I put back on looked brand new, but the only thing is the EGR valve itself.... I cleaned it but never opened it up (the plastic part) to check on it. Very well could have some issues in there. Also, to add, after doing the cleaning back when I did, I have constantly kept an eye on engine temps, and I have not seen anything go above about 199 degrees F. It's usually stable around 195-197, only spiking a bit higher under heavy engine load (uphill, heavy accelerating, etc.).