2.1.2 Commanders
Some units and characters are noted as being
commanders. Commanders can order up to three
formations of troops to follow them when they make an
assault, as long as all the formations have at least one unit
within 5cm of a unit from the commander’s formation.
Make a single initiative roll for all the formations,
counting a -1 modifier if any have Blast markers. If the test
is failed then the commander’s formation receives a Blast
marker and must take a hold action, but the other
formations are unaffected (and may take an action later in
the turn).
If the test is passed then all three formations may take an
engage action. Treat the three formations as if they were
a single formation for all rules purposes for the duration
of the assault. A 2D6 roll is used to resolve a combined
assault. If the attackers lose then each formation is
broken. If they win then each formation receives a
number of Blast markers equal to the casualties it suffered
in the combat.

An eldar player elects to retain the initiative with their Avatar, using the commander ability to combine with a guardian formation. Should the initiative test be take with or without the -1 retain penalty as the 'combined' formation has farsight.

The after that, the player retains for the 3rd time, this time using a guardian formation to combine with an aspect formation. Is this test at initiative 1 (from aspects) or 2 (guardians) before modifiers?

And is the second situation unique to the Eldar?

Consider the following situation (Section 2.1.2 below for reference).

An eldar player elects to retain the initiative with their Avatar, using the commander ability to combine with a guardian formation. Should the initiative test be take with or without the -1 retain penalty as the 'combined' formation has farsight.

So this is going to get an FAQ?

These are good points, and I am won over to the "you can't do that" side. But for the sake of discussion I'd point out that:

a) You can use another command ability more than once each turn, "Leader".
b) Staying with "Leader", the way it behaves for Space Marines also affects the value of the ability.

So this is going to get an FAQ?

Q: Can a Commander give Assault
orders to a several formations even if
the Commander himself isn’t in charge
range?
A: Yes. The Commander issues the orders
for the Combined Assault before the charge
move is made. If he issues the order
successfully (ie, passes his action test),
then his formation and the other two are
treated as one large formation for the
Assault.
This would mean that neither the
Commander nor any units from his
formation would need to get within 15cm
of the enemy so long as at least one unit
from the combined formation does so. Note
that the Commander and the units in his
formation would be bound by the
coherency rules, so would need to end the
charge with at least one unit within 5cm of
one unit from at least one of the other
formations.