Please refer to the extract from the code. As i understand from the code, Since you already have separate cable trays, so it is allowed.
392.20 Cable and Conductor Installation.(A) Multi conductor Cables Rated 600 Volts or
Less. Multi conductor cables rated 600 volts or less shall be
permitted to be installed in the same cable tray.
(B) Cables Rated Over 600 Volts. Cables rated over 600
volts and those rated 600 volts or less installed in the same
cable tray shall comply with either of the following:
(1) The cables rated over 600 volts are Type MC.
(2) The cables rated over 600 volts are separated from the
cables rated 600 volts or less by a solid fixed barrier of
a material compatible with the cable tray.
Referencing 300.3(C)(2) below:
(2) Over 1000 Volts, Nominal. Conductors of circuits rated
over 1000 volts, nominal, shall not occupy the same equipment
wiring enclosure, cable, or raceway with conductors of circuits
rated 1000 volts, nominal, or less unless otherwise permitted in
300.3(C)(2)(a) through 300.3(C)(2)(d).
(a) Primary leads of electric-discharge lamp ballasts insulated
for the primary voltage of the ballast, where contained
within the individual wiring enclosure, shall be permitted to
occupy the same luminaire, sign, or outline lighting enclosure
as the branch-circuit conductors.
(b) Excitation, control, relay, and ammeter conductors
used in connection with any individual motor or starter shall
be permitted to occupy the same enclosure as the motor-circuit
conductors.
(c) In motors, transformers, switchgear, switchboards, control
assemblies, and similar equipment, conductors of different
voltage ratings shall be permitted.
(d) In manholes, if the conductors of each system are permanently
and effectively separated from the conductors of the
other systems and securely fastened to racks, insulators, or other
approved supports, conductors of different voltage ratings shall
be permitted.
Conductors having nonshielded insulation and operating
at different voltage levels shall not occupy the same enclosure,
cable, or raceway.
What conductors are being referred to in the red sentence? Conductors over 1000 volts that are nonshielded? Does this seem somewhat in conflict to permitting 1000 volts or less conductors occupy the same enclosure, cable or raceway as permitted by (a) through (d)?