When using C-x C-- or C-x C-+ to change display font size, table heading
becomes misaligned. I've tracked down the problem to
`org-table-separator-space` variable. The space inserted by it retains old
size which skews alignment. Replacing it with " " via setq fixes it for a
session. I tried to override it via `org-hook` and `orgtbl-mode-hook` but
it somehow gets reset back to old value a first time I press C-c C-c to
re-alight the table!

You can see the screenshot here:

https://stackoverflow.com/questions/54951495/org-mode-table-header-formatting-not-properly-aligned


Emacs  : GNU Emacs 25.2.2 (x86_64-pc-linux-gnu, GTK+ Version 3.22.21)
 of 2017-09-22, modified by Debian
Package: Org mode version 9.2.2 (9.2.2-elpa @
/home/lord/.emacs.d/elpa/org-20190304/)

current state:
==============
(setq
 org-tab-first-hook '(org-babel-hide-result-toggle-maybe
                      org-babel-header-arg-expand)
 org-speed-command-hook '(org-speed-command-activate
                          org-babel-speed-command-activate)
 org-occur-hook '(org-first-headline-recenter)
 org-metaup-hook '(org-babel-load-in-session-maybe)
 org-log-done 'time
 org-confirm-shell-link-function 'yes-or-no-p
 org-from-is-user-regexp "\\<Vadim Zaliva\\>"
 org-src-mode-hook '(org-src-babel-configure-edit-buffer
                     org-src-mode-configure-edit-buffer)
 org-agenda-before-write-hook '(org-agenda-add-entry-text)
 org-babel-pre-tangle-hook '(save-buffer)
 org-mode-hook '(#[0 "\300\301\302\303\304$\207"
                   [add-hook change-major-mode-hook org-show-all append
local] 5]
                 #[0 "\300\301\302\303\304$\207"
                   [add-hook change-major-mode-hook
org-babel-show-result-all
                    append local]
                   5]
                 org-babel-result-hide-spec org-babel-hide-all-hashes
                 #[0 "\301\211\207"
                   [imenu-create-index-function org-imenu-get-tree] 2]
                 (lambda nil (org-bullets-mode 1))
                 (lambda nil (setq org-table-separator-space " ")))
 org-bibtex-headline-format-function #[257 "\300\236A\207" [:title] 3
"\n\n(fn ENTRY)"]
 org-archive-hook '(org-attach-archive-delete-maybe)
 org-cycle-hook '(org-cycle-hide-archived-subtrees
org-cycle-show-empty-lines
                  org-optimize-window-after-visibility-change)
 org-confirm-elisp-link-function 'yes-or-no-p
 org-metadown-hook '(org-babel-pop-to-session-maybe)
 org-link-parameters '(("id" :follow org-id-open)
                       ("eww" :follow eww :store org-eww-store-link)
                       ("rmail" :follow org-rmail-open :store
                        org-rmail-store-link)
                       ("mhe" :follow org-mhe-open :store
org-mhe-store-link)
                       ("irc" :follow org-irc-visit :store
org-irc-store-link
                        :export org-irc-export)
                       ("info" :follow org-info-open :export org-info-export
                        :store org-info-store-link)
                       ("gnus" :follow org-gnus-open :store
org-gnus-store-link)
                       ("docview" :follow org-docview-open :export
                        org-docview-export :store org-docview-store-link)
                       ("bibtex" :follow org-bibtex-open :store
                        org-bibtex-store-link)
                       ("bbdb" :follow org-bbdb-open :export org-bbdb-export
                        :complete org-bbdb-complete-link :store
                        org-bbdb-store-link)
                       ("w3m" :store org-w3m-store-link) ("file+sys")
                       ("file+emacs") ("doi" :follow org--open-doi-link)
                       ("elisp" :follow org--open-elisp-link)
                       ("file" :complete org-file-complete-link)
                       ("ftp" :follow
                        (lambda (path) (browse-url (concat "ftp:" path))))
                       ("help" :follow org--open-help-link)
                       ("http" :follow
                        (lambda (path) (browse-url (concat "http:" path))))
                       ("https" :follow
                        (lambda (path) (browse-url (concat "https:" path))))
                       ("mailto" :follow
                        (lambda (path) (browse-url (concat "mailto:"
path))))
                       ("news" :follow
                        (lambda (path) (browse-url (concat "news:" path))))
                       ("shell" :follow org--open-shell-link))
 org-agenda-files '("~/Dropbox/Notes/personal.org"
                    "~/Dropbox/Notes/codeminders.org"
                    "~/Dropbox/Notes/research.org")
 org-clock-out-hook '(org-clock-remove-empty-clock-drawer)
 )


-- 
"Hated by fools, and fools to hate, be that my motto and my fate"
(Jonathan Swift)