A custom system changes the shape of the cost. Not always the size, but the shape, and the shape is what matters over five years.
You pay to build it once. That's a capital expense, and it lands in one or two fiscal years. After that, your recurring costs are hosting, a database, backups, and whatever maintenance and improvement work you want. Hosting an internal application for a hundred users is cheap. It's measured in tens or low hundreds of dollars a month, and it barely moves when you add users, because the cost driver is data and traffic, not headcount.
So the curve flattens. Going from forty users to ninety in a system you own costs you roughly nothing in licensing. You create fifty accounts. That's it. Compare that to the $30,000 a year of additional subscription you'd owe for the same growth.
Run the five-year comparison honestly. On the subscription side, add up your projected seat count each year, multiply by the annual per-user price, and apply a realistic renewal increase. Include every tool the custom system would replace. Include the integration middleware you pay for to keep those tools talking. Include the consultant you hire every time you need a new workflow configured.
On the ownership side, put your build cost in year one, hosting for all five years, and a realistic maintenance budget. Then compare totals. For a company that's growing headcount and running three or four overlapping platforms, ownership usually wins somewhere in year two or three. For a company of twelve that isn't growing, it usually doesn't. Do the math for your numbers, not for the ones in an article.
The most useful number in this analysis is your projected seat count in year three. Not today's count. Subscription costs are a bet on your own growth, and you're the one who knows the hiring plan.