From my annotations in The Topical Guide to The Complete Peter Leroy (so far) (the page references are to that version of Peter Leroy's work, not to the books): 

Peter uses this (overuses, I think) as an almost universal metaphor for complexity. Many others would do just as well. 

See: 
Introduction, page 3: a bowl of soup 
Introduction, page 23: that big book about myself, that book as rich and various as a good clam chowder 
Introduction, page 38: Like most things, this process can be compared to the making of a good clam chowder 
Introduction, page 42: Basically, then, there are two kinds of stuff in chowder: chunky bits and the broth that links them, that makes them components of a chowder and not just a bowl of chunky bits 
Reservations Recommended, page 520: something like bouillabaisse -- with shellfish, saffron, all that good stuff 
LITTLE Follies, page 723: In the manner of a chowder . . . the emotion that we call love is a bewildering and varied concoction 
MMS(aD): Did you ever taste a chowder without guts? 

See also: 
Herb 'n' Lorna, page 346: If we are concocting an American social dish, this is where it's cooking, and it's something like a hearty stew or chowder, with chewy bits in every spoonful, not all of them familiar. 
Reservations Recommended, page 196: Forgive us, Father, but we were brought up in N*w Y*rk, raised on the clam chowder known hereabouts as M*nh*tt*n. Our first impression of what Bostonians consider the real goods, chowderwise, was that it must be a tonic for ulcer victims. 
LITTLE Follies, page 188: everyday chowder is nothing to sneer at, and there are many occasions when it is just the thing - cold, blustery, rainy days, for instance 
LITTLE Follies, page 240: it has always seemed to me that life, in several respects at any rate, is . . . like clam chowder 
LITTLE Follies, page 942: I still keep trying to write that big book about myself, that book as rich and various as a good clam chowder, loaded with useful and interesting information, hilarious anecdotes, recherch´e allusions, philosophical speculations, intriguing stories, clever word play, important themes, striking symbols, creative sex, intricate diagrams, mouth-watering recipes, big ideas -- 

In addition, see:

What a Piece of Work I Am: She taught me . . . how very many things can be explained in terms of clam chowder.
Making My Self . . . and Dinner: A Good Chowder Is a Big Chowder (So Make Extra, Just in Case)
Classified Advertising: Best Clam Chowder Recipe

A Topical Guide to the Complete Peter Leroy (so far) is a work of fiction. The characters, incidents, dialogues, settings, and businesses portrayed in it are products of the author’s imagination and are not to be construed as real. Any resemblance to actual events or persons, living or dead, is entirely coincidental. 

All rights reserved. No part of this guide may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or by any information storage and retrieval system, without permission in writing from the author. 

Portions of A Topical Guide to the Complete Peter Leroy (so far) were first published by Voyager, Inc., as part of The Complete Peter Leroy (so far).

The illustration at the top of the page is an adaptation of an illustration by Stewart Rouse that first appeared on the cover of the August 1931 issue of Modern Mechanics and Inventions. The boy at the controls of the aerocycle doesn’t particularly resemble Peter Leroy—except, perhaps, for the smile.