The article states that the quantity that was measured was the distance from the Earth to Mercury:
"By very precisely tracking the distance to MESSENGER from Earth, the collaboration was able to measure the change in the Earth-Mercury distance over the several years of observation. This amounted to about two meters, and this was the first nonzero measurement of the changing gravitational parameter of the sun (keeping in mind the distance between them is at least 77,000,000,000 meters). They found that the sun’s gravity was getting proportionally weaker by 6.13±1.47×10−146.13±1.47×10−14 per year (61 parts per quadrillion), and thus the solar system is slowly expanding as well."
However, we know that tidal effects from friction will gradually slow down the orbit of a small body orbiting around a larger body, even if the small body is a solid mass such as the Earth's moon.
For example, quoting from
https://phys.org/news/2015-09-moon.html :
"Gravitational coupling between the moon and the bulge nearest the moon acts as a torque on Earth's rotation, draining angular momentum and rotational kinetic energy from Earth's spin. In turn, angular momentum is added to the moon's orbit, accelerating it, which lifts the moon into a higher orbit with a longer period.
As a result of this, the distance between Earth and moon is increasing, and Earth's spin is slowing down. Measurements from lunar ranging experiments with laser reflectors (which were left behind during the Apollo missions) have found that the moon's distance to Earth increases by 38 mm (1.5 in) per year."
The equations for orbital mechanics always assume that there is conservation of energy in the system, but over long periods of time tiny effects such as heat dissipated by tidal friction make this assumption incorrect.
Has anyone estimated the effects of tidal friction on the Sun and the eight major planets?
Mercury would experience a greater effect because it's deeper in the gravitational field of the Sun, but the fact that Earth has oceans and an atmosphere and Mercury does not might well create much more friction. Liquids and gases dissipate tidal energy faster than solids. IOW, the Sun-Earth distance might increase faster than the Sun-Mercury distance, thus explaining the increasing gap between the two planets without requiring any changes to the way that gravity works.
The fact that Earth also has a large Moon would also affect the amount of dissipation of the total kinetic energy of the Earth, although that may not affect the distance from Mercury to Earth directly.