Ye I used to think like that but belive me it is far better and you still can use MDF spoil boards for quick or awkward jobs. The only difference is I don't ever have to surface the bed when it's critical to flat and true. I find because of 45mm centres 90% of the time find a suitable hole or pocket. Drilling is the most trouble some for me but I often pocket holes anyway(If not loads holes) so it's not a big deal.

One of the things I will often do when cutting several jobs that all have different needs is mix both MDF, HDPE and my card board spacer trick and use offsets G54, G55 etc.

I have my bed divided up into area's and have spot drilled small registration dot's so I know the 0,0 of each offset. Then I just fasten each particular job down using which ever method best suits the job lining the board up with the ref marks, line the material up with the corner of the board then in CAM/code I always have the part just in from 0,0 stand back and let it rip.
Depending on the jobs and time etc I don't always do it in one large piece of code, sometimes I'll have seperate code for each job just with the different offset coded in. This way I don't lose too much time unclamping re-clamping etc and can set the next job off straight away because I've set up the next offset while the previous job was cutting, just set the Z0 which is a 10 second affair with tool probe and away it goes again. . . It's quite efficeint.
The other good thing about clamping MDF or HDPE boards is because of the accurate and parallel tracks and offsets I can easily remove and replace the board with work still attached. Sometimes I'll do really long jobs that can be 15-20+ hours long so some times don't want to leave the machine on unattended so pick a suitable point to stop the code but then some times find I need the machine for something else in the mean time.!. . . doing it this way I can clear the table for the new job but still be perfectly back in position and carry on at anytime.

Like I say " FOR ME " it really has been a good improvement and worth the investment but everyone has different needs and ways of working.