How unusual is it for remotely piloted aircraft to fly through commercial or general aviation airspace?
In the US, the main operators of large UAS (i.e. non CFR Part 107 aircraft) are Air National Guard (MQ-9) and the Department of Homeland Security (Customs and Boarder Protection, also MQ-9). Here is a table from the Pentagon on how many missions UAS flew domestically in FY2018. (Note that these are "missions" and do not include other types of operations such as training or flight test, see below.)



A report from OIG published in 2014 lists a total of 5,102 flight hours by CBP in FY2013 (which is supposed to be closer to 26,000+, hence the OIGs investigation). Air National Guard also operates MQ-9 domestically for frequent training missions and contractors such as General Atomics Aeronautical Systems, Inc. and Northrop Grumman operate a fleet of capital aircraft at their respective training centers (e.g. Grand Forks). Lastly, of course, NASA also flies UAS. An example of how such missions are executed is described in this NASA report on the Western States Fire Missions starting on page 30.

So on your question about frequency: Assuming that the sum of all those aircraft result in ~5x number of flight hours, you'd be looking at something like 25,000 yearly flight hours in the US National Airspace System of large Remotely piloted aircraft. This is likely on the low side given the OIGs observation about the operational tempo of the CBP fleet.

So Why Is This Demonstration Relevant?

You may ask: if we're already operating these aircraft without chase planes, what was so special about this flight? It was the ability to fly a UAS without a chase plane without first having to climb to Class A airspace. 

FAA Notice 8900.227 stipulates the requirements for how to obtain operational approval for an unmanned aircraft; specifically, it states:


  ... compliance with the see-and-avoid requirement [is a] primary concerns in UAS operational approvals leading to [...] the use of observers [to maintain] flight separation and collision avoidance or ‘segregation’;


In the case of a flight with a chase aircraft, that visual observer is onboard the chase aircraft. This is also where the "Visual Line of Sight Requirement" comes from - the observer/pilot must be able to see the aircraft during the operation. 
There is one exception in N8900.227 for the visual observer (VO) requirement:


  VOs are not required in Class A airspace [...]


As a result, so far operations of the above-mentioned agencies occur almost exclusively in Class A airspace; i.e. above 18,000ft. Since those entities are either government agencies or contracting with a government agency, access to restricted airspace is straight forward where these aircraft can circle up or down to and from Class A airspace. In the case CBP and Global Hawk operations in Grand Forks there is a Temporary Flight Restriction that enables this access to Class A airspace without the need of a chase aircraft below 18,000ft. 

This type of operation is incredibly inefficient though (imagine if manned aviation had to operate like that). As a result, and that is what makes this NASA flight unique, the ability to use an onboard system to detect and avoid other aircraft (i.e. a Detect and Avoid System) when operating in airspace other than Class A, in particular Class E below 10,000ft where "non-cooperative" aircraft operate removes a list of operational limitations. From N8900.227 again:


  b. Risk Mitigation. While considerable work is ongoing to develop a certifiable detect, sense, and avoid system as an AMOC with the see-and-avoid aspect of §§ 91.113 and 91.115, no current solution exists.


The "considerable work" mentioned refers to this NASA project - and the flight was the capstone demonstration to show equipment in fact can serve as an Alternate Means of Compliance (AMOC) when operating outside of Class A airspace.