On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life was published in London by John Murray in 1859. As you can see from the title page reproduced at Wikipedia, the title appears in all-capital letters in at least five different font sizes: the largest font is used for the words "THE ORIGIN OF SPECIES"; the second-largest for "BY MEANS OF NATURAL SELECTION"; the third-largest for the opening word "ON"; the fourth-largest for "PRESERVATION OF FAVOURED RACES IN THE STRUGGLE FOR LIFE"; and the fifth-largest (that is, the smallest) for "OR THE."
Viewed in isolation, the title might be read in a number of ways, including one reading in which the words "BY MEANS OF" are assumed to be implicitly repeated between "OR" and "THE" in the fourth line of the title page:
ON THE ORIGIN OF SPECIES BY MEANS OF NATURAL SELECTION, OR [BY MEANS OF] THE PRESERVATION OF FAVOURED RACES IN THE STRUGGLE FOR LIFE.
But titles in the alternative are common in books published between 1600 and 1900, and they show no tendency to use implicit parallelism and phrase sharing between alternatives. A Google Books search for the simple phrase "or the" yields hundreds of matches for book titles that use the words as a transition device between the lead title and its alternative. Here are sixteen examples that appeared at roughly 20-year intervals between 1600 and 1900 (inclusive):
Nicholas Breton, PASQVILS Mistresse: Or THE WORTHIE AND vnworthie woman (1600)
Charles Butler, The Feminine Monarchie: OR THE HISTORIE OF BEES· SHEWING Their admirable Nature, and Properties, Their Generation, and Colonies, Their Gouernment, Loyaltie, Art, Inductrie, Enemies, Warres, Magnanimitie, &c. Together With the right ordering of them from time to time : And the sweet profit arising thereof. (1623)
James Howell, ΔΕΝΔΡΟΛΟΓΙΑ. DODONA'S GROVE, OR, THE VOCALL FORREST (1640)
John Reeve & Lodowick Muggleton, A DIVINE Looking-glass: OR, The third and last Testament of our Lord JESUS CHRIST, Whose personal Residence is seated on his Throne of Eternal Glory in another world; ... (1656/1661)
Thomas Mall, A CLOUD OF WITNESSES OR, THE Sufferers Mirrour, Made up of The SWANLIKE-SONGS, and other Choice Passages of several MARTYRS and CONFESSORS, to the end of the Sixteenth Century, in their Treatises, Speeches, Letters, Prayers, &c. ... (1677)
Anonymous, Anguis in Herba : OR THE Fatal Consequences of a Treaty with FRANCE. (1702)
John Worlidge, A Compleat SYSTEM of Husbandry and Gardening ; OR, THE Gentleman's Companion, In the BUSINESS and PLEASURES OF A COUNTRY LIFE. (1716)
Marcomire, THE Unfortunate Dutchess: OR, THE Lucky GAMESTER. A NOVEL, Founded on a true STORY. (1739)
George Watkins, The Compleat Brewer ; OR, The ART and MYSTERY OF BREWING EXPLAINED. (1760)
Marmaduke Stalkartt, NAVAL Architecture OR THE Rudiments and Rules OF SHIP BUILDING Exemplified in a Series of Draughts and Plans. WITH OBSERVATIONS Tending to the further improvement of that Important Art. (1781)
George Faber, A DISSERTATION ON THE MYSTERIES OF THE CABIRI; OR THE GREAT GODS OF PHENICIA, SAMOTHRACE, EGYPT, TROAS, GREECE, ITALY, AND CRETE; BEING An Attempt to deduce the several Orgies of ISIS, CERES, MITHRAS, BACCHUS, RHEA, ADONIS, AND HECATE, FROM AN Union of the Rites commemorative of the Deluge with the Adoration of the Host of Heaven. Volume 2. (1803)
John LORD Somers, THE SECURITY OF ENGLISHMEN'S LIVES; OR THE TRUST, POWER, AND DUTY OF THE GRAND JURIES OF ENGLAND, EXPLAINED ACCORDING TO THE FUNDAMENTALS OF THE ENGLISH GOVERNMENT, AND THE DECLARATIONS OF THE SAME MADE IN PARLIAMENT BY MANY STATUTES. (1821)
John Campbell, THE MARTYR OF ERROMANGA. OR, THE PHILOSOPHY OF THE MISSIONS, ILLUSTRATED FROM THE Labours, Death, and Character OF THE LATE REV. JOHN WILLIAMS. (1842)
Isabella Duncan, PRE-ADAMITE MAN ; or, The Story of our Old Planet and its Inhabitants, told by Scripture & Science. (1860)
Harriet Beecher Stowe, A DOG'S MISSION; OR, THE STORY OF THE OLD AVERY HOUSE. AND OTHER STORIES. (1880)
Herbert Webber, "XENIA, OR THE IMMEDIATE EFFECT OF POLLEN, IN MAIZE." (1900)
Given the tradition of alternative titles that these and many other instances from the seventeenth through nineteenth centuries reflect, it can scarcely be doubted that Darwin was offering his title in just such a way: on the one hand as On the Origin of Species by Means of Natural Selection, and on the other as The Preservation of Favoured Races in the Struggle for Life." As in the many examples cited above, the or in Darwin's title simply links the first and second alternative titles together.
In the alternative titles listed above, I found no evidence of parallel-structured wording in which the second alternative borrowed elements from the first alternative without explicitly repeating them.