The rules suggest "yes" (if the recent errata is taken literally)
As explained in detail here, call lightning controls where the lightning bolts hit that are called down by the caster. That question and its answers exposed some of the ambiguities that you ask about. Salient features of the spell:
Call Lightning / Range: 120 feet / Duration: Concentration, Up to 10 minutes
A storm cloud appears in the shape of a cylinder that is 10 feet
tall with a 60-foot radius, centered on a point you can see 100 feet
directly above you. [...]
If the caster stays immobile, then the location of that cylinder does
not move.
When you cast the spell, choose a point you can see within range. {120'} A
bolt of lightning flashes down from the cloud to that point. [...]
If you are outdoors in stormy conditions when you cast this spell, the spell gives you control over the existing storm instead of creating a
new one. Under such conditions, the spell’s damage increases by 1d10.
It favors option 1a (see below) (Old text in brackets, now text in bold).
CALL LIGHTNING 3 conjuration • Casting Time: 1 action • Range: 120
feet • Components: V S • Duration: Up to 10 minutes •
• A storm cloud appears in the shape of a cylinder that is 10 feet
tall with a 60-foot radius, centered on a point you can see {100
feet}within range directly above you. The spell fails if you can’t
see a point in the air where the storm cloud could appear (for
example, if you are in a room that can’t accommodate the cloud).
• When you cast the spell, choose a point you can see {within
range}(under the cloud). A bolt of lightning flashes down from the
cloud to that point. Each creature within 5 feet of that point must
make a Dexterity saving throw. A creature takes 3d10 lightning damage
on a failed save, or half as much damage on a successful one. On each
of your turns until the spell ends, you can use your action to call
down lightning in this way again, targeting the same point or a
different one. If you are outdoors in stormy conditions when you cast
this spell, the spell gives you control over the existing storm
instead of creating a new one. Under such conditions, the spell’s
damage increases by 1d10. {snip}
Option 1: Move the caster, move the source
One way to answer your question is to consider that the character moves; in this case, the frame of reference is the caster. The druid (or tempest cleric) is thus able to call down lightning from any part of the natural storm within range. (100' over her head). Since the caster did not have to create the ersatz storm, there isn't a problem of the basic version's summoned mini-storm's location being the limit on how far away an enemy can be. Using this logic, wherever there is natural storm, there is a place to call down lightning from. Caster moves, and from a point 100' over her head, reaches out and touches a creature 120' away, or less, with a lightning bolt.
Option 1a: Anywhere under the storm
The November 2018 errata takes this a step further. If the enemy is under the cloud (natural) it can be struck, due to the "under the cloud" update shown in the bold.
Option 2: Pick a spot and shoot from there
If the above option seems to be too powerful for a given DM / table, then pick a spot in the existing storm, concentrate on that, and shoot from there. In this case, the frame of reference is the place within the storm that the caster begins to concentrate on when casting the spell initially. The benefit in this case is restricted to the added 1d10 damage benefit from using natural lightning. Using this logic, it is the act of concentration on that spot in that part of the natural storm, to call down the lightning from the storm, that limits where the bolts can strike enemy creatures.
Which one do you think is more fun, or a better fit for our table?
Pick that one. Discuss with your DM if you are a player in this case.
One of the nice feature of D&D 5e is how much is not specified, such as cases like this. This is consistent with the general 5e theme that rulings > rules, and that the rules serve the game, and the people at the table.
And as a referee, the DM interprets the rules ... (DMG, p. 4)
As a referee, the DM acts as a mediator between the rules and the
players. [...] The rules don't account for every possible situation
that might arise during a typical D&D session. (DMG p. 5)
Make a ruling and play on.