После анализа dmesg двух вариантов сборки с PAE и без, выяснил, что единственное отличие в порядке подключения ACPI.
Кусок лога без PAE:Copyright (c) 1992-2008 The FreeBSD Project.
Copyright (c) 1979, 1980, 1983, 1986, 1988, 1989, 1991, 1992, 1993, 1994
The Regents of the University of California. All rights reserved.
FreeBSD is a registered trademark of The FreeBSD Foundation.
FreeBSD 6.4-RELEASE #1: Thu Jul 2 14:42:10 MSD 2009
root@ctlot.vladfond.ru:/usr/obj/usr/src/sys/SMP
Timecounter "i8254" frequency 1193182 Hz quality 0
CPU: Intel(R) Xeon(TM) CPU 2.80GHz (2790.96-MHz 686-class CPU)
Origin = "GenuineIntel" Id = 0xf27 Stepping = 7
Features=0xbfebfbff<FPU,VME,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,PSE36,CLFLUSH,DTS,ACPI,MMX,FXSR,SSE,SSE2,SS,HTT,TM,PBE>
Features2=0x4400<CNXT-ID,xTPR>
Logical CPUs per core: 2
real memory = 4025942016 (3839 MB)
avail memory = 3937476608 (3755 MB)
ACPI APIC Table: <PTLTD APIC >
FreeBSD/SMP: Multiprocessor System Detected: 4 CPUs
cpu0 (BSP): APIC ID: 0
cpu1 (AP): APIC ID: 1
cpu2 (AP): APIC ID: 6
cpu3 (AP): APIC ID: 7
ioapic0 <Version 2.0> irqs 0-23 on motherboard
ioapic1 <Version 2.0> irqs 24-47 on motherboard
ioapic2 <Version 2.0> irqs 48-71 on motherboard
kbd1 at kbdmux0
...
Кусок лога с PAE:
Copyright (c) 1992-2008 The FreeBSD Project.
Copyright (c) 1979, 1980, 1983, 1986, 1988, 1989, 1991, 1992, 1993, 1994
The Regents of the University of California. All rights reserved.
FreeBSD is a registered trademark of The FreeBSD Foundation.
FreeBSD 6.4-RELEASE #6: Thu Jul 2 16:59:04 MSD 2009
root@ctlot.vladfond.ru:/usr/obj/usr/src/sys/SMP_PAE
ACPI APIC Table: <PTLTD APIC >
Timecounter "i8254" frequency 1193182 Hz quality 0
CPU: Intel(R) Xeon(TM) CPU 2.80GHz (2790.96-MHz 686-class CPU)
Origin = "GenuineIntel" Id = 0xf27 Stepping = 7
Features=0xbfebfbff<FPU,VME,DE,PSE,TSC,MSR,PAE,MCE,CX8,APIC,SEP,MTRR,PGE,MCA,CMOV,PAT,PSE36,CLFLUSH,DTS,ACPI,MMX,FXSR,SSE,SSE2,SS,HTT,TM,PBE>
Features2=0x4400<CNXT-ID,xTPR>
Logical CPUs per core: 2
real memory = 6710886400 (6400 MB)
avail memory = 6302982144 (6010 MB)
FreeBSD/SMP: Multiprocessor System Detected: 4 CPUs
cpu0 (BSP): APIC ID: 0
cpu1 (AP): APIC ID: 1
cpu2 (AP): APIC ID: 6
cpu3 (AP): APIC ID: 7
ioapic0 <Version 2.0> irqs 0-23 on motherboard
ioapic1 <Version 2.0> irqs 24-47 on motherboard
ioapic2 <Version 2.0> irqs 48-71 on motherboard
kbd1 at kbdmux0
...
Т.е. отличие только в месте расположения строки:
ACPI APIC Table: <PTLTD APIC >