My understanding is that clearance and creepage requirements in safety standards apply for the separation between user-accessible parts and potentially hazardous circuits, not between two hazardous circuits.
I have access to the IEC 61010 standard, which I believe is very nearly identical to UL 61010. In IEC 61010-1, section 6.4.2, the requirement is
If ENCLOSURES or PROTECTIVE BARRIERS provide protection by limiting access, CLEARANCES and CREEPAGE DISTANCES between ACCESSIBLE parts and HAZARDOUS LIVE parts shall meet the requirements of 6.7 and the applicable requirements for BASIC INSULATION. [emphasis added]
and in section 6.4.3
CLEARANCES, CREEPAGE DISTANCES and solid insulation forming BASIC INSULATION between
ACCESSIBLE parts and HAZARDOUS LIVE parts shall meet the requirements of 6.7. [emphasis added]
Since presumably neither of your two 1000 V wires is accessible, these requirements don't apply, and not meeting the clearance and creepage distances between these wires shouldn't prevent you from meeting a 61010 standard.
However, you might still want to prevent arcs between these two circuits (for example, when one is powered but the other one isn't), and the clearance and creepage values from 61010 may be a reasonable guide to how to do that.
One point in IEC 61010 that I'm not entirely clear on the interpretation of is in section 6.7:
Insulation between circuits and ACCESSIBLE parts (see 6.2) or between separate circuits consists of a combination of CLEARANCES, CREEPAGE DISTANCES and solid insulation.
This would tend to indicate that creepage and clearance should be observed between "separate circuits", but I don't see any "shall" clause saying when this must be provided.
I am not advising you on whether your design is safe and you should have your design checked by a licensed engineer in your jurisdiction before you offer it for use by the public.