The flexibility (that is almost never used much as it is usually so difficult to actually do and often requires you to pay very expensive company contractors to be able to see the added fields in reports, etc.) usually comes with a huge price tag in performance, awkward design and general dislike. These products almost never take the time to properly define the requirements (relying instead on their problematic "flexibility") and thus you get project management software that doesn't even have a field for clientclients (what company is big enough to need project management software that costs over 100K doesn't have internal and external clients that you need to be able to filter on?) and other such nonsense.
The last COTS product we bought was so bad that our developers offered to fix our old company-designed product on their own time to give it what they thought they were getting (but actually didn't get) in this very expensive PM software we bought. 100% of the users of this system hated it because of the bad design and worse performance. It did not provide anyone in the company with what they needed in terms of reports or documentation and we could not get rid of this piece of trash because we had spent too much money on it. We now have less documentatiodocumentation of our devlopmentdevelopment process and what we do put inthein the system takes devs longer to actually put in and takes managers exponentially more time to manage.
Then there was the horrible HR COTS product to do timesheets with that we couldn't even get the people entering the original data to figure out how to change a supervisor when the person moved to a new boss or the old one left. Kind of hard to get my leave approved when the person who was two supervisors previous to my current one and who left the company over a year ago is my approver and no one can figure out how to fix that. And the equally bad performance review software that lost the mid-year reviews and that wouldn't print a version where you could see your rating on each item next to your boss's rating (who would want to see both?) and which didn't actually give enough space to list your accomplishments for the year (why ask me what they were if I can't list them?). Of course, those HR products were so badly designed our web developers were laughing at them when we were trained on how to use them.
I have almost never used a COTS product in an Enterprise organization that worked well or did the job it was supposed to do according to its marketing. And I've seen a lot of these products through the years. The exception would be Red-Gate's products (great products and stellar support and no I don't work for them) and a few small specialized tools, but never a big enterprisyenterprise-type thing.
Reinventing the wheel (writing your own version rather than using one of these products) is fine when the wheel is misshappenmisshapen and wobbly to begin with.