How about if the funds to take on a mission are based on the expected opposition, rather than what the player has? So there might be several contracts available, but the PC force might have to pass on most of them because their force isn't physically set up for that mission.
Total up the cost (in C-Bills or BV) of the opposition, multiply that by a percentage, and that is the contract fee.
I.e. a player force might have 4 Mechs, 1 light, 2 medium, and 1 heavy.
They have to pass up the city patrol contract because it needs 300 infantry
They may have to pass up the base assault because intel says there are four Heavy or Assault Mechs guarding it
They have to pass up the 'rapid escort' mission because they have to be capable of speed 8+ to keep up with the package and avoid being caught by the previous owners
If the player has good Tactics, Strategy, and Leadership skills, they can roll for advantages to let them take on the more profitable missions. I.e. tactics can govern which side of the map the players come in on or even which map is used, Strategy means one or more of the enemy Mechs are placed where the player wants instead of where the enemy wants, Leadership might cause a local force to join them to provide spotting in case of double-blind rules, etc.
So the PC Mech force might not be initially accepted for the base assault mission, but their skills could allow them to pull off the mission successfully.
To set this up properly, the players offer a contract amount they would like to go for, and that is the base for the GM's budget. Dice rolls choose what missions are available, PC dice rolls adjust those options, player preference and dice rolls choose the skill level of their opposition, enemy force composition, etc. The more that remains unknown, the more the PC force will get paid, but a note is added that the unknown part should be designed to deal with weaknesses in the PC force.
Once the players have the selected mission and the options, the GM is able to select the force that they will face. The base amount of funds the players will go for is multiplied by a constant, and the GM uses that as the shopping list. Mechs, vehicles, ambushes, infantry, off-board artillery, air strikes, pilot P/G skills, pilot quirks,
Unit Quirks, existing damage, all are purchased by the GM. The smaller categories can be within 10% of the expected budget amount, while the overall is to be within 5% of the original budgeted amount.
(The problem is determining that constant, similar to the existing issue for how much compensation for a contract and units utilized)
So you could have a much larger Pirate force raiding than expected, but several of them are suffering from damage and can be popped easily. A Clan force is smaller, but the Clan pilots are elite and have all sorts of nasty quirks (i.e. the pilot gets +3 damage to autocannon fire).
(The nice part about using the contract amount instead of compensating for the costs of the player unit, is that if the players want to bring along 'profitable' units, they still have to pay maintenance on them, while the money needed for maintenance is directly used to purchase units to attack them with. By using a cost-plus method, a playermight find that a certain unit pays a lot of money just for existing, allowing the merc company to make a lot of money on the contracts with little risk.)