I spent 17 years of my career working in Systems Integration and I feel your pain! As you stated in your post, most of your unexpected cost overage is related to physical installation labor and the need to purchase/rent site or hardware specific tools (e.g. Fiber termination kits, trenching machines, boring tools, special 6ft. drill bits, lift trucks, etc.) for infrastructure (cable, conduit, power, poles, concrete, etc.) installation.
I was able to reduce and control our installation costs by eliminating our in-house general labor pool and, depending on the type of work, subcontracting an Electrical, General Contractor or Network Infrastructure company to install the necessary infrastructure and physical hardware for my security related projects. If you aren't already competing with these folks for projects you will know that the live in the infrastructure world and have a labor pool that can perform this work efficiently, so let them do it for you.
A good subcontractor will typically offer you labor costs at hourly/daily/weekly rates for manpower to install your system (you can also have them terminate and connect the cable to your edge devices). Assuming they have taken the time to inspect the job site with you and they understand your detailed and specific Scope of Work, they will provide you with a fixed number to install it for you.
It has been more than ten years ago now, but I was able to negotiate a rate of $2,750 per week for 2x men for a 35 Hour on-site work week with tools, ladders and truck for general installation labor for any of my Projects. The labor costs varied based on specific site requirements (i.e. trenching, fiber terminations, pole installation, etc.) but even then, the cost went up marginally and I wasn't on the hook to purchase or rent specialized equipment or tools, cost of gas, cost of vehicle, cost of insurance, cost of overtime. etc. I have no doubt that rates are more expensive these days but the key is that I had a FIXED LABOR COST and no hidden surprises with specialized installation tools because my sub covered it all.
If your subcontractor is able to save time on the installation (and they will), they make money. If they run over or need to purchase/rent a specific tool or machine to perform the installation, it's on them because they inspected the job site and provided you with a hard quote/number for your Scope of Work (be sure to have a paragraph about Change Orders in your SOW & contract with your sub!). You can/should also apply a "Project Management Fee" to your quotes to manage your subs and assign one of your full time staff to do it. You still have to send someone to site to make sure your sub following your installation SOW.
Send your existing in-house Technical Team to a Project Management class and have them focus on "Parts & Smarts" (i.e. Programming, Commissioning & Servicing your installed projects). Redirect, retrain, reduce, or eliminate your 'general' labor staff (those that do your non-skilled general labor) and assuming you can write a meaningful and detailed Scope of Work that covers everything you need to get done for the installation for your subcontractor, you will immediately reduce your installation costs and see your labor and general margins increase.
Finally - I would also recommend that you send your Sales and Technical Team to a Project Estimating class. This will ensure that they understand how to correctly look at and estimate labor to perform any Project as well as empower them to negotiate with your subcontractor to be certain that you are being quoted realistic labor numbers for the work you need done.
It worked for me.