Your neutrals are still connected to ground in the upstream disconnects. But that isn't the problem. The problem is about neutral current.
Unless your ATS switches the neutral (not common) then when you run the circuit for the interlocked generator breaker you are creating a parallel path for neutral current. This is a violation of 300.20 and will cause slight heating on any metal conduit. It could also potentially overload the neutral on the interlocked circuit between the panels, particularly when running on grid power.
Help me understand the issue you are seeing from 300.20.
300.20 Induced Currents in Ferrous Metal Enclosures or
Ferrous Metal Raceways.
(A) Conductors Grouped Together. Where conductors carrying
alternating current are installed in ferrous metal enclosures
or ferrous metal raceways, they shall be arranged so as to avoid
heating the surrounding ferrous metal by induction. To accomplish
this, all phase conductors and, where used, the grounded
conductor and all equipment grounding conductors shall be
grouped together.
Exception No. 1: Equipment grounding conductors for certain existing
installations shall be permitted to be installed separate from their associated
circuit conductors where run in accordance with the prouisions of
250.lJ0(C).
Exception No. 2: A singk conductor shall be permitted to be installed in
a ferromagnetic encwsure and used for skin-effect heating in accordance
with the prouisions of 426.42 and 427.47.
(B) Individual Conductors. Where a single conductor carrying
alternating current passes through metal with magnetic properties,
the inductive effect shall be mi.nimized by (1) cutting slots
in the metal between the individual holes through which the
individual conductors pass or (2) passing all the conductors in
the circuit through an insulating
Exception: In the case of circuits supplying vacuum or ekctric-discharge
lighting systems or signs or X-ray apparatus, the currents carried by the
conductors are so small that the inductive heating effect can be ignored
where these conductors are placed in metal enclosures or pass through
metal.
Informational Note: Because aluminum is not a magnetic metal,
there will be no heating due to hysteresis; however, induced
currents will be present. They will not be of sufficient magnitude
to require grouping of conductors or special treatment in passing
conductors through aluminum wall sections.