Back in this after time doing real work...
First, the whole view point for these rules should be put to re-thinking. For one, it is important to understand that these rules do not really work in terms of existing tournaments (no one is seriously running regiment on board with current scale and rules). Thus there is no reason to assume that there is a set "500 fantasy point" limit to build against.
Which is why tournaments are generally either:
-Pre-calibrated by the GM; or
-Based on BV, BattleForce points (which are BV-based,) or another criterion.
These IO rules are patterned after Mercenary's Handbook (/3055) and Field Manual: Mercenaries (/(Revised.)) As such, they can interact with Chaos Campaign, StratOps, and A Time of War to play forces that you intend to keep playing longer than single pickup games or CC tracks.
Second, these rules are going to be used when players either play a campaign or build enemy/ally formation. I said it before and say it again. It must be able to build a semi-random unit out of source book. There are also players who like to build their own unit and/or hire one for their campaign. Thus there must be a support to any and all possible troop combinations (say a WarShip and a Star League Mech division).
At this moment I can build a random Mech regiment with tables in SO (p 331 to 335) to create notional units. For example a Light Lance of 1 Medium and 3 Light Mechs. Then I simply roll using suitable RAT. This is BTW how to do a "believable" house unit.
You can arguably do so with IO rules, in one of two ways:
-Agree with your table that the RAT and pilot-skill random rolls
replace the availability roll, and pay either exact or generic cost for what you get; or
-Use the alternate finance rules (the Hanse Davion's 3025 AFFS example) of rolling 1d2 for having either spare cash or debt, then 2d6 for the number of months of peacetime opcost that you're ahead or behind to start.
Notice that lots of special abilities of house units can also simply be added to units making them more/less costly. For example Urban specialization, better logistics/recce/fire support etc.
That's partially implemented - the special abilities are only combat functions (initiative, piloting, gunnery, in various circumstances) and you can take two modifiers (either two -1s, two +1s, or one of each.) It also applies to your whole force.
Suggestion: In the older books, forces that had multiple companies sometimes had different abilities / modifiers for their subforces. For example, each of Wolf's Dragoons' five regiments had different modifiers; each battalion in Alpha Regiment might have different modifiers; and the companies within a given battalion might be different. This did not go "smaller" than the company level though.
While it's extra book-keeping for costs and keeping them straight in the TO&E, might this be revisited as an option?
For Clan forces, this would be at the Trinary level; for C*/WoB forces, at the... man, their units are funky... the level III, I guess, even though that's about a battalion, because their training tends to be even more standardised and coordinated.