I agree with all that Mike (alldigial) posted.
I have been using the Adafruit library for the BMP288 (and now the BMP290) baro chip. There are also a bunch of Factory Compensation values stored in the chip. These most be read out, converted to float and then used on every BMP2xx temperature and pressure reading,
The Baro's Altitude graph still does not look right. It is VERY Rare to have discontinuities (kinks) in pressure derived altitude. Only time I seen that is when Ejection Charge blows into the Baro chips compartment or total wrong vents holes that cause internal pressure changes from external source like wind or air speed.
The rocket has Mass and therefore Momentum so will not change speed quickly and altitude is integral of speed which changes slower. The Alt curve should be smooth.
The Accelerometer should be measured to obtain Calibration correction values in the lab (home).
Then code in the Accel offset and gain corrections and apply to each reading before subtracting Earth's G, etc.
The data sheet does say that mounting the chip (soldering) can change the factory calibration but is then stable. I have done this with the Accel chips I use and have gotten very good Accel, Veloc & distance integrating the Accel sensor.
I haven't seen your new code that obtain 'real' time intervals. Does this have enough precision (should be to at least 100us or better)?
One more suggestion... you have a lot of serial.prints in your code. These are huge time sucks, since serial is slow, so surround them with a flag you can turn off for your launch build and turn on for bench debugging.
Absolutely a good idea.
A good way to do this is with compiler directives.
Code:
#define debug_out // comment out to remove excess print statements
#ifdef debug_out
serial.prints(output value);
#endif
The Bigger picture:
All this data and code is great learning. However, for your finial goal of deploying air brakes I think the Baro Altitude will do the job.
Right now you have unknowns indicated by different measurement methods not matching. These do need to be addressed.
Have you considered a vacuum chamber to test Baro verse JL2? This would allow you to run many, many tests without going out and launching.
Accelerometer testing is harder. Best might be your soccer ball. Launching the soccer ball could be done with a lever (seesaw style) by placing ball on lower end and jumping on the high end.