If you are spooling files in such rapid succession that the time from one submission to the next is less than the time it takes the lpr command to execute, then surely SBR=SUBMIT2 is going to present the risk you've identified.
I'm not sure there is any simple solution though, since I'm not sure of the exact sequence of events in lpr receiving the submission and sending it to the output device.
SBR=SUBMIT2 causes the submitted processes (which are executing lpr) to run independently of the parent, so it is a bit like herding cats to force them to execute in a certain sequence.
As an aside, although there is good reason to assume that jobs should appear on the printer in the same order submitted, there is no good reason to assume that two print jobs submitted in contiguous sequence by one program will in fact appear contiguously on the printer. (That is, another print job from another process could squeeze in the middle.) To assume otherwise implies some kind of application-level mechanism to regulate print flow. If such a mechanism existed, then it might be better to address the chronological issue there as well, rather than in XCALL SPOOL, which has no understanding of the events taking place before or after this particular spool request, or those taking place simultaneously on other jobs.
That said, if it works ok without SBR=SUBMIT2, then perhaps a reasonable workaround is to turn that flag off when spooling, or on when you were using SUBMIT and otherwise wanted it.
For unknown reasons, the MIAMEX,MX_SBRFLG(123) call is not documented, but it works similarly to the MIAMEX, MX_GETOPTIONS and MX_SETOPTIONS, except that the first argument is an opcode (0=get, 1=set).
So, to retrieve the current SBR= flags and then set or clear the SUBMIT2 flag:
map1 sbrflags,b,4
define SBRF_SUBMIT2 = &h20000000 ! SBR=SUBMIT2
xcall MIAMEX, MX_SBRFLG, MXOP_GET, sbrflags ! retrieve
sbrflags = sbrflags or SBRF_SUBMIT2 ! set SUBMIT2
or
sbrflags = sbrflags and not SBRF_SUBMIT2 ! clear SUBMIT2
xcall MIAMEX, MX_SBRFLG, MXOP_SET, sbrflags ! set