The definition of GFR given in Wikipedia -
Glomerular filtration rate (GFR) is the volume of fluid filtered from the renal (kidney) glomerular capillaries into the Bowman's capsule per unit time.
Since it is difficult to measure the volume entering into each Bowman's capsule, as a proxy, we measure the clearance of a solute that we know isn't going to be absorbed or secreted. For that particular solute,
GFR = (Urine concentration x Urine flow)/ Plasma concentration
The GFR you obtain here is the sum total of volume of all the fluid filtered from all the renal (kidney) glomerular capillaries into all of the Bowman's capsule per unit time.
Obviously, a single Bowman's capsule can't receive 120ml every minute, it is microscopic!!
So yes, the GFR or eGFR we use in clinical practice is the sum total of the function of both the kidneys. In fact, before transplantation, although the left kidney is preferred from the donor (since it is easier for surgery having a longer renal vein), it is more ethical to estimate individual GFR for each kidney and preserving the better functioning kidney. And yes, the total GFR drops after donating a kidney, but the body has sufficient reserve to manage.
If you still have a tough time figuring that out, think of them as many separate taps opened to fill a bucket. One tap for each glomerulus. The net rate of flow is the sum of flow rate in all the taps. The kidney has million such taps! And the taps are being clogged one at a time in chronic kidney disease - decreasing the GFR. And in a transplant, half the taps are suddenly shut down in the donor! But since this is a healthy kidney, the donor adapts and slowly reaches ~70% of original GFR.