It's all fun and games... until a deadline looms.
OneNote is free and does not require an O365 subscription to use it. Regardless of which office suite used, I recommend OneNote for rich-content notes.
re: Pages/Word & SOP's. If these documents need to conform to things like ISO9000/9001 document control elements, then the iOS versions of Pages/Word will not be helpful.
re: Numbers/Excel & budgets, flowcharts, and inventory. For very basic functionality, these will handle the job fine. But anything beyond the basics, and it'll be a hard uphill slog. In general, working on spreadsheets larger than the iPad's screen is simply a very poor experience. For those times that I need to work on such a spreadsheet on my iPad Pro, I use Jump Desktop to remotely connect to my iMac and using a mouse and ASK, I'll work on the full version of Numbers and Excel. I keep the current working set of files on iCloud and/or OneDrive so that I have the flexibility to remotely work on my iMac.
re: Keynote/PowerPoint and presentations. Here is where both shine on the iPad Pro. They offer nearly all the functionality one needs for CREATING presentations. Where the iPad Pro becomes a liability is in PRESENTING. Depending upon your presentation style, you will find that it works perfectly or unusable. For my presentation needs, the iPad Pro falls quite a bit short... particularly in the support for presentation remote controls.
Thanks for the additional detail regarding what you'll need to do. My recommendation (assumes that your MBP is still functional) is for you to continue forward with your 12.9 iPad Pro purchase. Get the Smart Keyboard (if you haven't already).
Rather than use the iPad Pro to REPLACE your MBP, use it as an EXTENSION of it. Use the MBP to create any advanced-formatted documents but use the iPP for everything after that. Invest in Jump Desktop and Citrix X1 Mouse so that when you are out-and-about and need to do macOS-y things, you can use the iPP to remotely connect to your MBP and drive it with the ASK and X1 mouse as if you were sitting in front of it.
That is what I'm currently doing. Over time, the amount of times that I have to "fall-back" to remotely connect to my iMac is slowing decreasing. My hope is that with the release of iOS 11 and additional app updates, I'll be able to do all but the most advanced tasks on the iPP.
Along those lines, I've been experimenting with Chromebooks to see how well they serve the purpose of being an EXTENSION of my iMac. The results have been extremely interesting but a topic for another thread.