Hello Steve,
I will endeavor here, sorry for the brevity of this post...
At least for my typical post replies...
I am taking that by "blad or stud" you are referencing the "tenon" at the base of a post?
These are never embedded in concrete and the few times I myself have seen such take place it is the indication of a "novice" at best doing the work and/or a contractor that is ignorant of the proper methods or showing little respect for the craft and proper treatment of wood...
First, I meant not to sound condescending, yet seldom find the methodologies of "GC" to have much merit at all, and seldom give sound advice when regarding the proper procedures of timber frames. The method related is one of a form that some do manage to facilitate in a reasonable manner, yet I find typically there are much better modalities to apply in tectonically active regions. Both traditional (my preference) and modern methods exist with the first having a history that is well known going back millenia.
I would, before going further, suggest that no matter what method is selected that a PE be selected that is familiar with traditional Timber Framing (I can recommend one, but own my biases here is strong.) I bring this up as you had mentioned and "Engineer" and like many (not all) "GC" if they are not familiar with timber framing too often lack the knowledge and creativity to over "best practices" and usually fixate on what they know and understand.
As for the frame "lining up" on raising day, I can assure you if a well seasoned Timberwright is consulted to design and facilitate the project, such issues are rare if at all occurring...
I have used structural adhesives of all form and manner from polyurethan to advanced epoxies to only mechanical methods and...of course...only traditional ones that maybe only slightly augmented with modernity. With a proper PE, you will be in good hands I am sure...
I seldom use, do not like nor promote OPC cements and find there use more a "convenience" for contractors and the like than actual "good practice." All one has to do is look at the OPC infrastructure of modern times and see the many flaws and lacking durability of this material in so many ways...Our bridges, as just one limited example, are mostly falling apart when made with "modern cements/concretes," while something like the Brooklyn Bridge is still going strong after heavy use over its 150 plus year life...It is made of some wrought iron, stone and "natural cements"/lime mortars... I only bring it up for the sake of exploring all the option out there for a durable foundation...I own my bias on this subject, yet have many years of studying and examining this subject. I actually like the use of mortars, and cements, yet seldom (virtually never) see it done well or with the appropriate modalities and actual "good cement work" is virtually nonexistent. What we have is mediocre at best and only in use because of the industries that promote it and our own collective laziness to demand better from the industry...which is slowly changing...