Phase difference between voltage source's voltage and current
This is simply due to the passive sign convention used by LTSpice's current probe for the voltage source. By this convention, power sources such as voltage sources have negative power dissipation, which means that the source's current is negative when the voltage is positive and vice versa.

Notice the arrow on the current probe icon is pointing downward for this voltage source:



It also points downward for \$R_1\$:



The plotted currents are out of phase:



But obviously they are the same current, as in this circuit there is only one current path. They are just out of phase because they are taken in the opposite direction, as indicated by the probe icon.