Comparing with theories of polyphonic harmony, would you say there is an similarly systematic theory for rhythmical phrasing
In general it seems difficult to divide things with your bright line - harmony and rhythm are intrinsically bound to one another. How can you apply harmony correctly if you don't know the timing and rhythm of a piece of music? How can you study more than simple rhythms that aren't purely percussive, if you're not playing melodies with harmonies?
Having said, that I believe that your question can be answered by taking a look at this syllabus and other resources on the Berklee Site. Here's a good place to start:
Berkee College of Music -Jazz Arranging
Syllabus Lesson 1: Rhythm Section and One Solo Instrument: Smooth Jazz
Jazz Arranging: Understanding the Writing (Arranging) Process Focus
Levels, Melodic, Rhythmic, and Harmonic Functions Comping Functions
Writing for the Drum Set Arrangement Considerations in the Smooth
Jazz-Funk Style Front-Line Solo Instrument Characteristics
Lesson 2: Bebop and Hard Bop Bop and Hard Bop Jazz Arrangement
Analysis Two-Part Writing Techniques Voicings and Intervals
Introductions/Endings
Lesson 3: Solis and Working with Vocalists Historical Perspective
Two-Horns and use of Pads Punches and Counter Melodies Vocal Ranges
Melodic Manipulation Writing Solis
Lesson 4: Big Band Historical Combinations Primary, Secondary, and
Tertiary Focus Levels Cross Sectional Possibilities Open- and
Close-Position Chord Voicings Spread Voicings Upper Structure Triad
Voicings Unison Arrangements
Lesson 5: Writing for Large Jazz Ensemble Choosing the Soloists Solo
Feature Combo Within the Big Band Open Solo Sections Background
Figures
Lesson 6: Writing for Large Jazz Ensemble (Part 2) The Saxophone Soli
Writing the Soli Coupling The Sax Section Endings
Lesson 7: Writing for Three Horns and Rhythm Section History of the
Three-Horn Front Line Unison-Octave Splits Independent Lead with
Two-Voice Background Three-Part Harmonization The Harmonization
Process Highlighting the Melody Cluster Voicing Secondary Focus Beyond
the Head
Lesson 8: Three Horns and Rhythm Section; Funk and Fusion Modal
Characteristics The Music of The Crusaders The Music of The Brecker
Brothers Role Model Composition
Lesson 9: Writing for Five Horns 5-Part Voicings Close Position Double
Lead Voicing Guidelines Substitute Double Lead 5-Part Passing Chords
Latin Influences: Brazilian Latin Influences: Afro-Cuban
Lesson 10: Final Project: Large Ensemble Arrangement Arrangement
Planning Hooks Working With Clients Conceptualizing the Arrangement
The Music of Sammy Nestico The Music of Rob McConnell The Music of
Thad Jones "Variable" Instrumentation
Lesson 11: Final Project: Large Ensemble Arrangement (Part 2) Building
to a Climax The Music of Mark Harris Large Ensemble Arrangement
Analysis The Music of Bob Mintzer
Lesson 12: Large Ensemble Arrangement (Part 3) Treating the
Recapitulation Score Analysis Color Reharmonization The Music of Bob
Brookmeyer The Music of Maria Schneider Conceptualizing the Whole
Arrangement
Requirements Prerequisites Completion of Arranging: Advanced Horn
Writing or equivalent knowledge and experience in basic arranging
concepts, such as instrument ranges, chord spelling, voicing, and
harmonization is required. You should also know modes and related
chord scales. Knowledge of basic reharmonization techniques is
helpful, but not required. Recommended experience in a DAW of choice.