(Correct me if I'm wrong.)
You're wrong. You can enter the UK for up to six months per visit without a visa. In all other EU countries except Ireland, the limit is 90 days in any 180-day period. This is counted separately for each non-Schengen EU country and for the Schengen area.
Ireland is either 90 days or three months; I don't remember which. I ...
Does this include layovers?
Yes, if you are an alien that does not fullfill one of the conditions of section 2 and were physically present within the Schengen Area during the 14-day period preceding their entry, when the plane departed after 11:59 p.m. eastern daylight time on March 13, 2020
As a US citizen, what will be the impact of my layover?
You have a big problem.
You'll be referred for deportation (Source), but that is the least of your worries.
The fine for overstaying is PHP500 per month. If you have overstayed 18 years the fine will be over PHP100,000 (one hundred thousand); about US$2000. There will also be some administrative charges but they're small by comparison.
If you can't pay ...
You have to approach US embassy in Philipines and explain the situation. US embassy can help you getting a new passport and emergency loan to repatriate you back to USA.
But rest assured that you have to pay the amount back and US might restrict you from leaving USA until you paid back the amount.
CNN states that:
The ban, slated to begin on Friday, only applies to foreign nationals, not American citizens, their immediate family members and legal permanent residents.
Returning travelers will be screened prior to entering the US and asked to self-quarantine for 14 days.
This is also confirmed by The Telegraph and Euronews.
It doesn't appear ...
As you have booked connecting flights (they're on the same ticket/booking), given your itineraries, you will be checked through to your destination:
At the point of departure, your bags will be tagged with the final destination. You will not see them again until you reach it.
You will probably be issued boarding passes for both flights. In some cases, they ...
Most airports of the world have one or more international transit areas which are completely separated from domestic flights, and in which passengers connecting via that airport from and to other countries do not need to pass immigration and formally enter that country. If your flights are on a single booking, then your checked baggage will be transferred ...