From your photos, it looks like they have added a bracing strip along the bottom. This is quite common as it doubles the bottom edge space to the vertical panes have more silicon contact.
It would be extremely simple to add an adjacent patch beside this bracing strip. Just clean the area with a sharp scraper & methylated spirits then firmly place your patch without squeezing out all the silicon. Do try to silicon all gaps as algae and mulm will get in between otherwise and be impossible to remove. Not dangerous but very unsightly and easily avoided. Your patch does not need to be one piece but for such a small area, one piece would be best.
For many longer tanks (10 - 12 - 16 foot or more) it is common practice to have a split bottom. This helps with flex supposidly (but could be a cost savng measure) and these are butt joined with silicon. You would be doing the same thing within the tank. Not much different to relying on silicon to water proof and hold the bottom and sides of tanks.
Also the CNC is a nice option but a $3 glass cutter would suffice if you want to shorten sheets of glass.
And if you do want to remove the existing bottom brace (I would not), just tape it with cloth tape and give it a few taps with a metal hammer so it cracks, then scrape out. The tape just to catch the shards better. Use a steel mesh fish fillet glove for protection if you have one. The glass will be very sharp.
At the end of the day, if you don't feel comfortable repairing the tank then don't.