Hi, I am not sure if I can answer all question, at least trying.
Questions:
1) e500 branch-locking APU [mentioned in EB622 but could not find the instructions]
2) isel instruction(mentioned and described in many places)
3) saturation instructions for AutoSAR [mentioned in AN4802 but could not find specific instructions, is this just SPE?]
4) Enhanced Reservations APU [?]
5) Volatile Context Save/Restore APU [this one is described in EB696]
6) Cache Bypass Storage APU [?]
Could be lbcbx, lhcbx, lwcbx, and stwwtx, sthwtx, stbwtx mentioned in MPC5775KRM but no actual descriptions found.
7) MPU instructions [e200z7260n3 only?]
mpuwe, mpure, mpusync described in MPC5775KRM
8) EB689 "Additional SPE Instructions" [evfsmadd, ... efsnmsub]
supposedly available only in VLE on e200z3 and e200z6. What about e200z4?
9) e200z490 (AIOP) custom instructions
some intrinsic functions are described in CWAPPBTR, e.g Byte-Reversing, double/quad word loads and stores, math functions, cache bypass etc. but not the actual instructions. Another list is in AMF-DES-T1052
10) SPE 2.1(? I think I've seen it mentioned somewhere but can't find it now. is it EB689?)
Answers:
1) I have found description in the document below
https://www.nxp.com/docs/en/reference-manual/E500CORERM.pdf

and also in old version of EREF document (EREF 01/2004 Rev. 2). Unfortunately I don't know architecture of all platforms (only e200) so I don't know whether it is used somewhere. Current revision of EREF document does not include the description (EREF_RM Rev. 1 06/2014).
2) You may find it in EREF_RM:
https://www.nxp.com/files-static/32bit/doc/ref_manual/EREF_RM.pdf

3) No, these instructions are described in the EREF_RM manual, it is not SPE instruction set. One example below:

4) These are following 4 instructions, again EREF_RM manual

5) EB696 mentions all these instructions even with opcodes.
6) Yes, these are the isntruction, but there is more in this category:

Unfortunately I haven't found any public description. If you need more info, please create new case and I could possibly send you more info if you have valid NDA (Non-disclosure agreement) with NXP.
7) As I know all devices having CMPU what's all MPC57xx devices excluding MPC5777c and MPC5775B/E according to my knowledge.
8, 10)


SPE2.1 specification is not publicly available, see answer no.6.