Aah, Belt! by Elfman

Gregson suspects this puzzle by Elfman is another in the string of recent puzzles which will produce divided opinion between those who spotted the finishing twist instantly and those (Gregson for one!) who stared at it for days before spotting the obvious in one of those d'oh moments.

The initial letters of 26 clues, when taken in alphabetical order of the extraneous letters in those clues, give "es o u en de i en se ach a em be e ar es", which can be interpreted as "sound in Chambers" using the pronunciation of letters as given in Chambers. The ordering of letters in the diagonals was therefore the alphabetical order of pronunciation. Thus the major diagonal contains AHRBDWEFXLMNS and the minor diagonal contains IJGKQOECTUVYZ, with the E taking the place of the P which is to be omitted. The title of the puzzle consists of the letters of ALPHABET, minus the P, arranged in thematic order.

The extra letters in 26 clues are shown highlighted in bold.

1 Peculiar charm of anonymous novel with no name (5)
AROMA (A (anonymous) + ROMAN (novel) minus N (name))
5 Ex-Soviet spies wandering Zen's paths (8)
11 Alternately throw off and expel (4)
HOOF (even letters of THROW OFF)
12 East and West have displayed this uneasy amenity (6)
13 Upsetting dark circle in dish (4)
OKRA (anag of ARK + O (circle))
14 Mountain has beginning (5)
ALPHA (ALP (mountain) + HA)
15 By drinking have toast (4)
OVEN (ON (by) round VE (have - 've)
17 Genus of birds from here and there in Spain and France (6)
AQUILA (AQUI (here in Spanish) + LA (there in French))
18 Equip with Yemen's crown: TAJ? (4)
ARMY (ARM (equip) + Y (first letter of Yemen))
20 Edinburgh's 15 grasped by you once (3)
OON (hidden)
22 Bird found around water (6, two words)
SEA MEW (SMEW (bird) round EA (water) &lit)
24 Copper one's almost entirely wedge-shaped (6)
CUNEAL (CU (copper) + NE + ALL (entirely) minus last letter)
26 See KB (not Q as usual) placed thus according to rule, then evenly set up (13)
29 Dingbat's Scottish guard dog (6)
WEIRDO (WEIR (guard) + DO)
32 Sadness of heartless farewell in French (6)
FADEUR (FR (French) round ADIEU (farewell) minus middle letter)
35 And not, certainly not, right (3)
NOR (NO (certainly not) + R (right))
36 Obstacle removal keeps this clear (4)
LERE (hidden)
37 Eagle perhaps made with half cut back mashy? (6)
HAWKED (HAWK (eagle perhaps) + half of MADE rev)
41 Scandinavian girl into composing epics (4)
INGE (hidden)
42 School in Europe nurtured artists' beginnings here (5)
SIENA (first letters of words, semi &lit))
43 Sartre's soul includes zone for his mistress? (4)
AMIE (AME (soul in French) round I (one))
44 Managed to find project about swearing (6)
JURANT (JUT (project) round RAN (managed))
45 It's granny that shows lack of understanding (4)
ANAN (A (it) + NAN (granny))
46 One strange endless ceremony taking year to produce rainmaking material (8)
IODYRITE (I (one) + ODD (strange) minus last letter + RITE (ceremony) round Y (year))
47 Ill-composed strain for lively tunes (5)
RANTS (anag of STRAN)

1 Euclid may have mingled with others here in past eras (6)
AGORAS (AGO (past) + RAS)
2 Astronomer overturned central aspect of astronomy (4)
OORT (hidden rev)
3 Drove around a kingdom (4)
OAB (MOB (drove) round A)
4 Naval admiral has a right to yield aft a distance (4)
AFAR (AF (naval admiral) + A + R (right))
5 A swale is pale in colour (6)
SALLOW (double def)
6 Hacking rocket's tip off propels explosive probe (6)
7 Do something for space Henry laid on once up north (7)
ENHANCE (EN (space) + H (Henry) + ANCE (once))
8 Restlessly anxious - descriptive of American people (6)
9 Excitable dog often is clumsy player (5)
AYELP (anag of PLAYE)
10 Cattle initially never associate in regions (7)
ZONALLY (ZO (cattle) + N (first letter of never) + ALLY (associate))
16 Escaped delirious fever (4)
FREE (anag of FEER)
19 Expert shows mothery wine (5)
MAVIN (MA (mother) + VIN (wine))
21 Deconstruct the early English laugh (5)
TEHEE (anag of THE + EE (early English))
23 Eat up all but one odd piece (3)
END (DINE (eat) minus I (one) rev)
25 One among Spanish Association (3)
UNA (double def - one in Spanish, United Nations Association)
26 People saw horrible depressions (7)
SWAHILI (anag of SAW + HILI (depressions))
27 In poor condition company lost circular mouldings (7)
TONDINI (anag of CONDITION minus CO (company))
28 Nurse likes spacing out half of sinsemilla with such temptation (4)
30 Closing of newspaper retail establishment after book's lost suggests corruption (6)
RAKERY (R (last letter of newspaper) + BAKERY (retail establishment) minus B (book))
31 Swirling mottled cloth (6)
32 Touch queen near the head, not below skirt (6)
FRINGE (FINGER (touch) with R (queen) moved from the bottom to near the head)
33 Is staggering to include British in people that are revolting (6)
REBELS (REELS (is staggering) round B (British))
34 Loved one needed after financial institution loses a thousand - it's there for the
picking (5)
BANJO (BANK (financial institution) minus K (thousand) + JO (loved one))
38 A crater from an explosion shows up in Iraq-American engagement (4)
MAAR (hidden rev)
39 Woody plant one's not found in wood (4)
LANA (LIANA (woody plant) minus I (one))
40 Top female country (4)
OMAN (WOMAN (female) minus first letter)