This is an interesting perspective. From what I've seen / heard from others, it's generally better to adapt processes to the off-the-shelf tool than to try and customize or build from scratch to accommodate your bespoke processes (especially in the business operations realms). For one, the organization is likely less unique than you think, and those bespoke processes are as often a function of some early employee's preference as it is a genuinely good reason. For another, customizing software is not just a one time cost, since every subsequent update / upgrade is likely to require additional work (or at least testing). And finally, in most cases the closer you are to a vanilla, standard process, the more likely you are to stay in compliance with local laws and regulations.
Though I suppose it's possible that the imbalance is just due to the fact that it is much harder to quantify the costs of using a suboptimal (for you) process than it is to look at the procurement contract for a custom solution.